Variant rs977096 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_145306.3(FAM241B):c.-104+324A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.22 in 1,298,406 control chromosomes in the GnomAD database, including 33,363 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.17 ( 2658 hom., cov: 33)

Exomes 𝑓: 0.23 ( 30705 hom. )

Consequence

FAM241B
NM_145306.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.110

Variant links:

Genes affected

FAM241B (HGNC:23519): (family with sequence similarity 241 member B) Predicted to be integral component of membrane. Predicted to be active in intracellular membrane-bounded organelle. [provided by Alliance of Genome Resources, Apr 2022]

FAM241B links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.006044477).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.231 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE
FAM241B	NM_145306.3 linkuse as main transcript	c.-104+324A>G		intron_variant		ENST00000373279.6
FAM241B	XM_005269606.3 linkuse as main transcript	c.1A>G	p.Met1?	start_lost	1/4
FAM241B	XM_005269608.4 linkuse as main transcript	c.-36+324A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FAM241B	ENST00000373279.6 linkuse as main transcript	c.-104+324A>G		intron_variant		1	NM_145306.3	P1	Q96D05-1
FAM241B	ENST00000421716.1 linkuse as main transcript	c.1A>G	p.Met1?	start_lost	1/4	2
FAM241B	ENST00000491890.1 linkuse as main transcript	n.63+324A>G		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes

AF:

0.171

AC:

25974

AN:

151992

Hom.:

2655

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0779

Gnomad AMI

AF:

0.0800

Gnomad AMR

AF:

0.159

Gnomad ASJ

AF:

0.158

Gnomad EAS

AF:

0.0380

Gnomad SAS

AF:

0.243

Gnomad FIN

AF:

0.219

Gnomad MID

AF:

0.136

Gnomad NFE

AF:

0.230

Gnomad OTH

AF:

0.168

GnomAD3 exomes

AF:

0.189

AC:

27357

AN:

144800

Hom.:

3014

AF XY:

0.197

AC XY:

15329

AN XY:

77936

show subpopulations

Gnomad AFR exome

AF:

0.0703

Gnomad AMR exome

AF:

0.135

Gnomad ASJ exome

AF:

0.159

Gnomad EAS exome

AF:

0.0333

Gnomad SAS exome

AF:

0.251

Gnomad FIN exome

AF:

0.222

Gnomad NFE exome

AF:

0.226

Gnomad OTH exome

AF:

0.178

GnomAD4 exome

AF:

0.227

AC:

259793

AN:

1146296

Hom.:

30705

Cov.:

AF XY:

0.228

AC XY:

128262

AN XY:

562082

show subpopulations

Gnomad4 AFR exome

AF:

0.0705

Gnomad4 AMR exome

AF:

0.137

Gnomad4 ASJ exome

AF:

0.160

Gnomad4 EAS exome

AF:

0.0329

Gnomad4 SAS exome

AF:

0.255

Gnomad4 FIN exome

AF:

0.227

Gnomad4 NFE exome

AF:

0.236

Gnomad4 OTH exome

AF:

0.200

GnomAD4 genome

AF:

0.171

AC:

25981

AN:

152110

Hom.:

2658

Cov.:

AF XY:

0.169

AC XY:

12605

AN XY:

74372

show subpopulations

Gnomad4 AFR

AF:

0.0776

Gnomad4 AMR

AF:

0.159

Gnomad4 ASJ

AF:

0.158

Gnomad4 EAS

AF:

0.0379

Gnomad4 SAS

AF:

0.243

Gnomad4 FIN

AF:

0.219

Gnomad4 NFE

AF:

0.230

Gnomad4 OTH

AF:

0.169

Alfa

AF:

0.201

Hom.:

2102

Bravo

AF:

0.159

TwinsUK

AF:

0.230

AC:

852

ALSPAC

AF:

0.226

AC:

871

ExAC

AF:

0.189

AC:

3946

Asia WGS

AF:

0.160

AC:

556

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_addAF

Benign

-0.62

BayesDel_noAF

Benign

-0.52

CADD

Benign

7.9

DANN

Benign

0.45

Eigen

Benign

-0.94

Eigen_PC

Benign

-1.2

FATHMM_MKL

Benign

0.0014

LIST_S2

Uncertain

0.90

MetaRNN

Benign

0.0060

MetaSVM

Benign

-1.0

MutationTaster

Benign

1.0

PROVEAN

Benign

-0.44

REVEL

Benign

0.11

Sift

Pathogenic

0.0

ClinPred

0.0024

GERP RS

-4.2

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.060

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over