10-123098521-T-C

Variant names:

• chr10-123098521-T-C
• rs10510121

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 0.981 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.981 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

Gnomad4 AFR AF: 0.996

Gnomad4 AMR AF: 0.975

Gnomad4 ASJ AF: 0.997

Gnomad4 EAS AF: 0.815

Gnomad4 SAS AF: 0.981

Gnomad4 FIN AF: 0.990

Gnomad4 NFE AF: 0.983

Gnomad4 OTH AF: 0.984

Alfa AF: 0.976 Hom.: 5519

Bravo AF: 0.979

Asia WGS AF: 0.900 AC: 3130 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10510121; hg19: chr10-124858037;