7-68587782-G-C

Variant names:

• chr7-68587782-G-C
• rs10499796

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 0.0779 in 152,196 control chromosomes in the GnomAD database, including 568 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 0.078 (568 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.167
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.108 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: 0.0779 AC: 11852 AN: 152078 Hom.: 567 Cov.: 32

Gnomad AFR AF: 0.0216

Gnomad AMI AF: 0.171

Gnomad AMR AF: 0.0697

Gnomad ASJ AF: 0.0654

Gnomad EAS AF: 0.0453

Gnomad SAS AF: 0.0780

Gnomad FIN AF: 0.116

Gnomad MID AF: 0.114

Gnomad NFE AF: 0.110

Gnomad OTH AF: 0.0852

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

GnomAD4 genome AF: 0.0779 AC: 11851 AN: 152196 Hom.: 568 Cov.: 32 AF XY: 0.0776 AC XY: 5774 AN XY: 74398

African (AFR) AF: 0.0216 AC: 897 AN: 41540

American (AMR) AF: 0.0695 AC: 1062 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.0654 AC: 227 AN: 3470

East Asian (EAS) AF: 0.0454 AC: 235 AN: 5174

South Asian (SAS) AF: 0.0777 AC: 374 AN: 4814

European-Finnish (FIN) AF: 0.116 AC: 1231 AN: 10582

Middle Eastern (MID) AF: 0.116 AC: 34 AN: 294

European-Non Finnish (NFE) AF: 0.110 AC: 7455 AN: 68018

Other (OTH) AF: 0.0852 AC: 180 AN: 2112

Alfa AF: 0.0565 Hom.: 51

Bravo AF: 0.0719

Asia WGS AF: 0.0460 AC: 163 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	5.7
DANN	Benign	0.63
PhyloP100		0.17

Splicing

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

Other links and lift over

dbSNP: rs10499796; hg19: chr7-68052769;