rs7916600

Positions:

• chr10-123271667-C-T

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 0.103 in 152,156 control chromosomes in the GnomAD database, including 873 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 0.10 (873 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.635

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.124 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.103 AC: 15712 AN: 152038 Hom.: 871 Cov.: 32

Gnomad AFR AF: 0.127

Gnomad AMI AF: 0.179

Gnomad AMR AF: 0.0943

Gnomad ASJ AF: 0.0945

Gnomad EAS AF: 0.0683

Gnomad SAS AF: 0.117

Gnomad FIN AF: 0.106

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.0915

Gnomad OTH AF: 0.106

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

GnomAD4 genome AF: 0.103 AC: 15730 AN: 152156 Hom.: 873 Cov.: 32 AF XY: 0.105 AC XY: 7793 AN XY: 74392

Gnomad4 AFR AF: 0.127

Gnomad4 AMR AF: 0.0941

Gnomad4 ASJ AF: 0.0945

Gnomad4 EAS AF: 0.0683

Gnomad4 SAS AF: 0.117

Gnomad4 FIN AF: 0.106

Gnomad4 NFE AF: 0.0915

Gnomad4 OTH AF: 0.108

Alfa AF: 0.0947 Hom.: 965

Bravo AF: 0.102

Asia WGS AF: 0.0840 AC: 290 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.95
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7916600; hg19: chr10-125031183;