chr7-82703579-G-T

Variant names:

• chr7-82703579-G-T
• rs10486980

Variant summary

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

The variant allele was found at a frequency of 0.0575 in 152,136 control chromosomes in the GnomAD database, including 326 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 0.057 (326 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.368
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0853 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: 0.0576 AC: 8750 AN: 152018 Hom.: 325 Cov.: 32

Gnomad AFR AF: 0.0156

Gnomad AMI AF: 0.109

Gnomad AMR AF: 0.0593

Gnomad ASJ AF: 0.0917

Gnomad EAS AF: 0.000579

Gnomad SAS AF: 0.0321

Gnomad FIN AF: 0.0471

Gnomad MID AF: 0.114

Gnomad NFE AF: 0.0872

Gnomad OTH AF: 0.0796

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

GnomAD4 genome AF: 0.0575 AC: 8746 AN: 152136 Hom.: 326 Cov.: 32 AF XY: 0.0549 AC XY: 4086 AN XY: 74382

African (AFR) AF: 0.0155 AC: 644 AN: 41534

American (AMR) AF: 0.0592 AC: 904 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.0917 AC: 318 AN: 3466

East Asian (EAS) AF: 0.000580 AC: 3 AN: 5172

South Asian (SAS) AF: 0.0313 AC: 151 AN: 4818

European-Finnish (FIN) AF: 0.0471 AC: 499 AN: 10588

Middle Eastern (MID) AF: 0.119 AC: 35 AN: 294

European-Non Finnish (NFE) AF: 0.0872 AC: 5927 AN: 67978

Other (OTH) AF: 0.0787 AC: 166 AN: 2108

Alfa AF: 0.0692 Hom.: 225

Bravo AF: 0.0578

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.39
DANN	Benign	0.26
PhyloP100		0.37

Splicing

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

Other links and lift over

dbSNP: rs10486980; hg19: chr7-82332895;