10-123098521-T-C

Variant names:

• chr10-123098521-T-C
• rs10510121

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 0.981 in 152,268 control chromosomes in the GnomAD database, including 73,292 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 0.98 (73292 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.77
• Publications: 2 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 (AFR) allele frequency at 95% confidence interval = 0.988 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.981 AC: 149192 AN: 152150 Hom.: 73232 Cov.: 31

Gnomad AFR AF: 0.996

Gnomad AMI AF: 0.958

Gnomad AMR AF: 0.975

Gnomad ASJ AF: 0.997

Gnomad EAS AF: 0.815

Gnomad SAS AF: 0.981

Gnomad FIN AF: 0.990

Gnomad MID AF: 1.00

Gnomad NFE AF: 0.983

Gnomad OTH AF: 0.984

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

GnomAD4 genome AF: 0.981 AC: 149313 AN: 152268 Hom.: 73292 Cov.: 31 AF XY: 0.980 AC XY: 72947 AN XY: 74442

African (AFR) AF: 0.996 AC: 41406 AN: 41568

American (AMR) AF: 0.975 AC: 14918 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.997 AC: 3463 AN: 3472

East Asian (EAS) AF: 0.815 AC: 4221 AN: 5178

South Asian (SAS) AF: 0.981 AC: 4719 AN: 4810

European-Finnish (FIN) AF: 0.990 AC: 10502 AN: 10610

Middle Eastern (MID) AF: 1.00 AC: 294 AN: 294

European-Non Finnish (NFE) AF: 0.983 AC: 66842 AN: 68014

Other (OTH) AF: 0.984 AC: 2074 AN: 2108

Alfa AF: 0.970 Hom.: 17196

Bravo AF: 0.979

Asia WGS AF: 0.900 AC: 3130 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.072
DANN	Benign	0.37
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs10510121; hg19: chr10-124858037;