7-81772113-G-T

Variant names:

• chr7-81772113-G-T
• rs11763015
• ENST00000771413.1:n.118-8110G>T

Variant summary

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

The ENST00000771413.1(ENSG00000300407):​n.118-8110G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0425 in 152,078 control chromosomes in the GnomAD database, including 177 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 0.043 (177 hom., cov: 32)
• Consequence: ENSG00000300407 ENST00000771413.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.720
• Publications: 4 publications found

Genes affected

ENSG00000300407 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0608 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
ENSG00000300407	ENST00000771413.1	n.118-8110G>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.0425 AC: 6463 AN: 151960 Hom.: 176 Cov.: 32

Gnomad AFR AF: 0.00914

Gnomad AMI AF: 0.0209

Gnomad AMR AF: 0.0434

Gnomad ASJ AF: 0.0530

Gnomad EAS AF: 0.0430

Gnomad SAS AF: 0.0667

Gnomad FIN AF: 0.0697

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.0565

Gnomad OTH AF: 0.0417

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

GnomAD4 genome AF: 0.0425 AC: 6466 AN: 152078 Hom.: 177 Cov.: 32 AF XY: 0.0440 AC XY: 3271 AN XY: 74328

African (AFR) AF: 0.00911 AC: 378 AN: 41496

American (AMR) AF: 0.0432 AC: 659 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.0530 AC: 184 AN: 3472

East Asian (EAS) AF: 0.0433 AC: 224 AN: 5172

South Asian (SAS) AF: 0.0668 AC: 322 AN: 4820

European-Finnish (FIN) AF: 0.0697 AC: 736 AN: 10564

Middle Eastern (MID) AF: 0.0306 AC: 9 AN: 294

European-Non Finnish (NFE) AF: 0.0565 AC: 3839 AN: 67996

Other (OTH) AF: 0.0456 AC: 96 AN: 2106

Alfa AF: 0.0164 Hom.: 10

Bravo AF: 0.0383

Asia WGS AF: 0.0590 AC: 204 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	2.8
DANN	Benign	0.86
PhyloP100		0.72

Splicing

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

Other links and lift over

dbSNP: rs11763015; hg19: chr7-81401429;