7-81773197-G-C

Variant names:

• chr7-81773197-G-C
• rs6942495
• ENST00000771413.1:n.118-7026G>C

Variant summary

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

The ENST00000771413.1(ENSG00000300407):​n.118-7026G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.532 in 151,966 control chromosomes in the GnomAD database, including 21,982 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 (21982 hom., cov: 32)
• Consequence: ENSG00000300407 ENST00000771413.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.73
• 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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.645 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000771413.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000300407	ENST00000771413.1		n.118-7026G>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.531 AC: 80701 AN: 151848 Hom.: 21954 Cov.: 32

Gnomad AFR AF: 0.652

Gnomad AMI AF: 0.298

Gnomad AMR AF: 0.496

Gnomad ASJ AF: 0.618

Gnomad EAS AF: 0.556

Gnomad SAS AF: 0.633

Gnomad FIN AF: 0.394

Gnomad MID AF: 0.677

Gnomad NFE AF: 0.476

Gnomad OTH AF: 0.560

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

GnomAD4 genome AF: 0.532 AC: 80775 AN: 151966 Hom.: 21982 Cov.: 32 AF XY: 0.529 AC XY: 39271 AN XY: 74244

African (AFR) AF: 0.652 AC: 27022 AN: 41452

American (AMR) AF: 0.495 AC: 7559 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.618 AC: 2143 AN: 3470

East Asian (EAS) AF: 0.557 AC: 2874 AN: 5164

South Asian (SAS) AF: 0.635 AC: 3064 AN: 4828

European-Finnish (FIN) AF: 0.394 AC: 4155 AN: 10534

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

European-Non Finnish (NFE) AF: 0.476 AC: 32309 AN: 67936

Other (OTH) AF: 0.558 AC: 1180 AN: 2114

Alfa AF: 0.507 Hom.: 2487

Bravo AF: 0.544

Asia WGS AF: 0.587 AC: 2040 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.17
DANN	Benign	0.42
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs6942495; hg19: chr7-81402513;