10-123271667-C-T

Variant names:

• chr10-123271667-C-T
• rs7916600

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 0.103 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
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.127 AC: 5262 AN: 41478

American (AMR) AF: 0.0941 AC: 1439 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0945 AC: 328 AN: 3470

East Asian (EAS) AF: 0.0683 AC: 354 AN: 5182

South Asian (SAS) AF: 0.117 AC: 564 AN: 4818

European-Finnish (FIN) AF: 0.106 AC: 1120 AN: 10586

Middle Eastern (MID) AF: 0.167 AC: 49 AN: 294

European-Non Finnish (NFE) AF: 0.0915 AC: 6224 AN: 68012

Other (OTH) AF: 0.108 AC: 227 AN: 2108

Alfa AF: 0.0977 Hom.: 1504

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
PhyloP100		-0.64

Splicing

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

Other links and lift over

dbSNP: rs7916600; hg19: chr10-125031183;