7-81774897-G-A

Variant names:

• chr7-81774897-G-A
• rs917183
• ENST00000771413.1:n.118-5326G>A

Variant summary

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

The ENST00000771413.1(ENSG00000300407):​n.118-5326G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.529 in 151,886 control chromosomes in the GnomAD database, including 21,746 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 0.53 (21746 hom., cov: 31)
• Consequence: ENSG00000300407 ENST00000771413.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.669
• Publications: 1 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=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.638 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.118-5326G>A		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.529 AC: 80273 AN: 151768 Hom.: 21719 Cov.: 31

Gnomad AFR AF: 0.644

Gnomad AMI AF: 0.299

Gnomad AMR AF: 0.493

Gnomad ASJ AF: 0.612

Gnomad EAS AF: 0.556

Gnomad SAS AF: 0.634

Gnomad FIN AF: 0.395

Gnomad MID AF: 0.677

Gnomad NFE AF: 0.476

Gnomad OTH AF: 0.556

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

GnomAD4 genome AF: 0.529 AC: 80344 AN: 151886 Hom.: 21746 Cov.: 31 AF XY: 0.527 AC XY: 39089 AN XY: 74216

African (AFR) AF: 0.644 AC: 26677 AN: 41414

American (AMR) AF: 0.492 AC: 7508 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.612 AC: 2124 AN: 3468

East Asian (EAS) AF: 0.557 AC: 2872 AN: 5156

South Asian (SAS) AF: 0.635 AC: 3054 AN: 4812

European-Finnish (FIN) AF: 0.395 AC: 4165 AN: 10544

Middle Eastern (MID) AF: 0.673 AC: 198 AN: 294

European-Non Finnish (NFE) AF: 0.476 AC: 32304 AN: 67916

Other (OTH) AF: 0.554 AC: 1169 AN: 2112

Alfa AF: 0.521 Hom.: 6556

Bravo AF: 0.541

Asia WGS AF: 0.587 AC: 2041 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	3.1
DANN	Benign	0.41
PhyloP100		0.67

Splicing

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

Other links and lift over

dbSNP: rs917183; hg19: chr7-81404213;