10-44258419-T-C

Variant names:

• chr10-44258419-T-C
• rs501120

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 0.241 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
• Publications: 138 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

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: 0.241 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

African (AFR) AF: 0.421 AC: 17475 AN: 41500

American (AMR) AF: 0.224 AC: 3422 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.213 AC: 739 AN: 3468

East Asian (EAS) AF: 0.347 AC: 1795 AN: 5178

South Asian (SAS) AF: 0.360 AC: 1733 AN: 4818

European-Finnish (FIN) AF: 0.156 AC: 1655 AN: 10602

Middle Eastern (MID) AF: 0.282 AC: 83 AN: 294

European-Non Finnish (NFE) AF: 0.136 AC: 9233 AN: 68010

Other (OTH) AF: 0.231 AC: 488 AN: 2112

Alfa AF: 0.181 Hom.: 9378

Bravo AF: 0.253

Asia WGS AF: 0.328 AC: 1141 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.5
DANN	Benign	0.42
PhyloP100		-0.15

Splicing

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

Other links and lift over

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