ENST00000648766.1:c.-398+411C>G

Variant names:

• chr8-11475455-G-C
• rs13257831
• ENST00000648766.1:c.-398+411C>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000648766.1(FAM167A):​c.-398+411C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.299 in 151,800 control chromosomes in the GnomAD database, including 8,906 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 0.30 (8906 hom., cov: 31)
• Consequence: FAM167A ENST00000648766.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0390
• Publications: 7 publications found

Genes affected

FAM167A (HGNC:15549): (family with sequence similarity 167 member A)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.928 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000648766.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FAM167A	ENST00000648766.1		c.-398+411C>G		intron	N/A	ENSP00000497969.1

Frequencies

GnomAD3 genomes AF: 0.299 AC: 45408 AN: 151682 Hom.: 8887 Cov.: 31

Gnomad AFR AF: 0.140

Gnomad AMI AF: 0.559

Gnomad AMR AF: 0.459

Gnomad ASJ AF: 0.217

Gnomad EAS AF: 0.950

Gnomad SAS AF: 0.373

Gnomad FIN AF: 0.336

Gnomad MID AF: 0.269

Gnomad NFE AF: 0.301

Gnomad OTH AF: 0.291

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

GnomAD4 genome AF: 0.299 AC: 45448 AN: 151800 Hom.: 8906 Cov.: 31 AF XY: 0.308 AC XY: 22858 AN XY: 74180

African (AFR) AF: 0.139 AC: 5768 AN: 41370

American (AMR) AF: 0.460 AC: 7015 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.217 AC: 751 AN: 3468

East Asian (EAS) AF: 0.950 AC: 4887 AN: 5142

South Asian (SAS) AF: 0.373 AC: 1795 AN: 4810

European-Finnish (FIN) AF: 0.336 AC: 3535 AN: 10516

Middle Eastern (MID) AF: 0.272 AC: 80 AN: 294

European-Non Finnish (NFE) AF: 0.301 AC: 20474 AN: 67922

Other (OTH) AF: 0.300 AC: 633 AN: 2112

Alfa AF: 0.150 Hom.: 276

Bravo AF: 0.309

Asia WGS AF: 0.621 AC: 2155 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.64
DANN	Benign	0.42
PhyloP100		0.039
PromoterAI		0.039	Neutral

Splicing

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

Other links and lift over

dbSNP: rs13257831; hg19: chr8-11332964;