Variant rs3101793 details in Genebe, Genetics Data Aggregator

Variant summary

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

The NR_026794.1(FAM238B):n.5477-82A>G variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.27 in 221,932 control chromosomes in the GnomAD database, including 8,641 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 0.26 ( 5743 hom., cov: 32)

Exomes 𝑓: 0.29 ( 2898 hom. )

Consequence

FAM238B
NR_026794.1 intron, non_coding_transcript

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.230

Variant links:

Genes affected

(HGNC:):

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 (BayesDel_noAF=-0.75).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.323 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FAM238B	NR_026794.1 linkuse as main transcript	n.5477-82A>G		intron_variant, non_coding_transcript_variant

Ensembl

Transcript	HGVSc	Effect	TSL
ENST00000423917.5 linkuse as main transcript	n.601-82A>G	intron_variant, non_coding_transcript_variant	5
ENST00000413288.1 linkuse as main transcript	n.263-82A>G	intron_variant, non_coding_transcript_variant	3
ENST00000434458.5 linkuse as main transcript	n.387-82A>G	intron_variant, non_coding_transcript_variant	3

Frequencies

GnomAD3 genomes

AF:

0.263

AC:

39961

AN:

151698

Hom.:

5739

Cov.:

show subpopulations

Gnomad AFR

AF:

0.140

Gnomad AMI

AF:

0.119

Gnomad AMR

AF:

0.258

Gnomad ASJ

AF:

0.301

Gnomad EAS

AF:

0.336

Gnomad SAS

AF:

0.255

Gnomad FIN

AF:

0.344

Gnomad MID

AF:

0.272

Gnomad NFE

AF:

0.321

Gnomad OTH

AF:

0.296

GnomAD4 exome

AF:

0.285

AC:

20013

AN:

70116

Hom.:

2898

AF XY:

0.292

AC XY:

12070

AN XY:

41392

show subpopulations

Gnomad4 AFR exome

AF:

0.143

Gnomad4 AMR exome

AF:

0.199

Gnomad4 ASJ exome

AF:

0.287

Gnomad4 EAS exome

AF:

0.335

Gnomad4 SAS exome

AF:

0.252

Gnomad4 FIN exome

AF:

0.329

Gnomad4 NFE exome

AF:

0.311

Gnomad4 OTH exome

AF:

0.304

GnomAD4 genome

AF:

0.263

AC:

39976

AN:

151816

Hom.:

5743

Cov.:

AF XY:

0.263

AC XY:

19505

AN XY:

74196

show subpopulations

Gnomad4 AFR

AF:

0.140

Gnomad4 AMR

AF:

0.257

Gnomad4 ASJ

AF:

0.301

Gnomad4 EAS

AF:

0.336

Gnomad4 SAS

AF:

0.254

Gnomad4 FIN

AF:

0.344

Gnomad4 NFE

AF:

0.321

Gnomad4 OTH

AF:

0.295

Alfa

AF:

0.288

Hom.:

785

Bravo

AF:

0.250

Asia WGS

AF:

0.261

AC:

908

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.75

CADD

Benign

5.6

DANN

Benign

0.92

Splicing

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