chr7-68587782-G-C

Variant names:

• chr7-68587782-G-C
• rs10499796

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.0216

Gnomad4 AMR AF: 0.0695

Gnomad4 ASJ AF: 0.0654

Gnomad4 EAS AF: 0.0454

Gnomad4 SAS AF: 0.0777

Gnomad4 FIN AF: 0.116

Gnomad4 NFE AF: 0.110

Gnomad4 OTH AF: 0.0852

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10499796; hg19: chr7-68052769;