10-44258419-T-C

Variant names:

• chr10-44258419-T-C
• rs501120

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 0.241 in 152,172 control chromosomes in the GnomAD database, including 5,676 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 0.24 (5676 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.148

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.416 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: 0.241 AC: 36632 AN: 152054 Hom.: 5651 Cov.: 33

Gnomad AFR AF: 0.421

Gnomad AMI AF: 0.0969

Gnomad AMR AF: 0.223

Gnomad ASJ AF: 0.213

Gnomad EAS AF: 0.346

Gnomad SAS AF: 0.359

Gnomad FIN AF: 0.156

Gnomad MID AF: 0.294

Gnomad NFE AF: 0.136

Gnomad OTH AF: 0.234

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

GnomAD4 genome AF: 0.241 AC: 36711 AN: 152172 Hom.: 5676 Cov.: 33 AF XY: 0.245 AC XY: 18235 AN XY: 74394

Gnomad4 AFR AF: 0.421

Gnomad4 AMR AF: 0.224

Gnomad4 ASJ AF: 0.213

Gnomad4 EAS AF: 0.347

Gnomad4 SAS AF: 0.360

Gnomad4 FIN AF: 0.156

Gnomad4 NFE AF: 0.136

Gnomad4 OTH AF: 0.231

Alfa AF: 0.164 Hom.: 4516

Bravo AF: 0.253

Asia WGS AF: 0.328 AC: 1141 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.5
DANN	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs501120; hg19: chr10-44753867; COSMIC: COSV70898760;