7-132003793-T-C

Variant names:

• chr7-132003793-T-C
• rs11767564
• ENST00000774478.1:n.272+631A>G

Variant summary

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

The ENST00000774478.1(ENSG00000300842):​n.272+631A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.867 in 152,202 control chromosomes in the GnomAD database, including 57,461 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 0.87 (57461 hom., cov: 32)
• Consequence: ENSG00000300842 ENST00000774478.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.13
• Publications: 2 publications found

Genes affected

ENSG00000300842 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.963 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000300842	ENST00000774478.1	n.272+631A>G		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.867 AC: 131882 AN: 152084 Hom.: 57399 Cov.: 32

Gnomad AFR AF: 0.917

Gnomad AMI AF: 0.750

Gnomad AMR AF: 0.881

Gnomad ASJ AF: 0.798

Gnomad EAS AF: 0.986

Gnomad SAS AF: 0.908

Gnomad FIN AF: 0.847

Gnomad MID AF: 0.820

Gnomad NFE AF: 0.831

Gnomad OTH AF: 0.852

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

GnomAD4 genome AF: 0.867 AC: 132007 AN: 152202 Hom.: 57461 Cov.: 32 AF XY: 0.869 AC XY: 64615 AN XY: 74398

African (AFR) AF: 0.917 AC: 38116 AN: 41554

American (AMR) AF: 0.882 AC: 13488 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.798 AC: 2765 AN: 3466

East Asian (EAS) AF: 0.986 AC: 5092 AN: 5166

South Asian (SAS) AF: 0.908 AC: 4377 AN: 4818

European-Finnish (FIN) AF: 0.847 AC: 8968 AN: 10588

Middle Eastern (MID) AF: 0.823 AC: 242 AN: 294

European-Non Finnish (NFE) AF: 0.831 AC: 56476 AN: 67998

Other (OTH) AF: 0.854 AC: 1799 AN: 2106

Alfa AF: 0.838 Hom.: 53209

Bravo AF: 0.871

Asia WGS AF: 0.938 AC: 3261 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.081
DANN	Benign	0.43
PhyloP100		-2.1

Splicing

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

Other links and lift over

dbSNP: rs11767564; hg19: chr7-131688552;