7-83858619-G-A

Variant names:

• chr7-83858619-G-A
• rs7802588

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.325 in 151,996 control chromosomes in the GnomAD database, including 13,008 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 0.33 (13008 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.22
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.45).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.69 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

Frequencies

GnomAD3 genomes AF: 0.325 AC: 49313 AN: 151878 Hom.: 12967 Cov.: 32

Gnomad AFR AF: 0.696

Gnomad AMI AF: 0.160

Gnomad AMR AF: 0.305

Gnomad ASJ AF: 0.142

Gnomad EAS AF: 0.692

Gnomad SAS AF: 0.135

Gnomad FIN AF: 0.105

Gnomad MID AF: 0.153

Gnomad NFE AF: 0.135

Gnomad OTH AF: 0.326

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

GnomAD4 genome AF: 0.325 AC: 49399 AN: 151996 Hom.: 13008 Cov.: 32 AF XY: 0.321 AC XY: 23826 AN XY: 74294

African (AFR) AF: 0.697 AC: 28869 AN: 41440

American (AMR) AF: 0.305 AC: 4651 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.142 AC: 492 AN: 3468

East Asian (EAS) AF: 0.693 AC: 3563 AN: 5144

South Asian (SAS) AF: 0.133 AC: 642 AN: 4818

European-Finnish (FIN) AF: 0.105 AC: 1111 AN: 10584

Middle Eastern (MID) AF: 0.154 AC: 45 AN: 292

European-Non Finnish (NFE) AF: 0.135 AC: 9197 AN: 67972

Other (OTH) AF: 0.323 AC: 683 AN: 2114

Alfa AF: 0.225 Hom.: 887

Bravo AF: 0.362

Asia WGS AF: 0.437 AC: 1518 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.45
CADD	Benign	17
DANN	Benign	0.51
PhyloP100		1.2

Splicing

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

Other links and lift over

dbSNP: rs7802588; hg19: chr7-83487935;