Variant rs247938 details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_198507.3(FAM174A):c.569+959T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.211 in 151,762 control chromosomes in the GnomAD database, including 3,644 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 0.21 ( 3644 hom., cov: 32)

Consequence

FAM174A
NM_198507.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.50

Variant links:

Genes affected

FAM174A (HGNC:24943): (family with sequence similarity 174 member A) Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

FAM174A 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=-0.8).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.258 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FAM174A	NM_198507.3 link	c.569+959T>C		intron_variant		ENST00000312637.5	NP_940909.1	Q8TBP5
FAM174A	XM_006714600.2 link	c.569+959T>C		intron_variant			XP_006714663.1

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Protein	UniProt
FAM174A	ENST00000312637.5 link	c.569+959T>C	intron_variant	1	NM_198507.3	ENSP00000307954.2	Q8TBP5
FAM174A	ENST00000505792.1 link	n.137+959T>C	intron_variant	3
FAM174A	ENST00000509040.1 link	n.584-23034T>C	intron_variant	3

Frequencies

GnomAD3 genomes

AF:

0.212

AC:

32081

AN:

151644

Hom.:

3644

Cov.:

show subpopulations

Gnomad AFR

AF:

0.263

Gnomad AMI

AF:

0.194

Gnomad AMR

AF:

0.142

Gnomad ASJ

AF:

0.120

Gnomad EAS

AF:

0.0868

Gnomad SAS

AF:

0.156

Gnomad FIN

AF:

0.232

Gnomad MID

AF:

0.123

Gnomad NFE

AF:

0.213

Gnomad OTH

AF:

0.187

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

AF:

0.211

AC:

32092

AN:

151762

Hom.:

3644

Cov.:

AF XY:

0.211

AC XY:

15635

AN XY:

74148

show subpopulations

Gnomad4 AFR

AF:

0.262

Gnomad4 AMR

AF:

0.142

Gnomad4 ASJ

AF:

0.120

Gnomad4 EAS

AF:

0.0870

Gnomad4 SAS

AF:

0.155

Gnomad4 FIN

AF:

0.232

Gnomad4 NFE

AF:

0.212

Gnomad4 OTH

AF:

0.186

Alfa

AF:

0.207

Hom.:

1599

Bravo

AF:

0.205

Asia WGS

AF:

0.115

AC:

400

AN:

3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.80

CADD

Benign

7.1

DANN

Benign

0.90

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

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