10-42558904-T-C

Variant names:

• chr10-42558904-T-C
• rs68055

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 0.777 in 151,744 control chromosomes in the GnomAD database, including 46,573 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 0.78 (46573 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -5.11
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.941 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: 0.777 AC: 117887 AN: 151628 Hom.: 46558 Cov.: 29

Gnomad AFR AF: 0.634

Gnomad AMI AF: 0.788

Gnomad AMR AF: 0.824

Gnomad ASJ AF: 0.783

Gnomad EAS AF: 0.963

Gnomad SAS AF: 0.773

Gnomad FIN AF: 0.725

Gnomad MID AF: 0.804

Gnomad NFE AF: 0.847

Gnomad OTH AF: 0.795

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

GnomAD4 genome AF: 0.777 AC: 117942 AN: 151744 Hom.: 46573 Cov.: 29 AF XY: 0.772 AC XY: 57294 AN XY: 74170

African (AFR) AF: 0.634 AC: 26178 AN: 41318

American (AMR) AF: 0.824 AC: 12559 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.783 AC: 2711 AN: 3464

East Asian (EAS) AF: 0.963 AC: 4966 AN: 5156

South Asian (SAS) AF: 0.774 AC: 3715 AN: 4798

European-Finnish (FIN) AF: 0.725 AC: 7610 AN: 10502

Middle Eastern (MID) AF: 0.813 AC: 239 AN: 294

European-Non Finnish (NFE) AF: 0.847 AC: 57566 AN: 67948

Other (OTH) AF: 0.796 AC: 1679 AN: 2108

Alfa AF: 0.771 Hom.: 2431

Bravo AF: 0.781

Asia WGS AF: 0.858 AC: 2984 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.18
DANN	Benign	0.14
PhyloP100		-5.1

Splicing

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

Other links and lift over

dbSNP: rs68055; hg19: chr10-43054352; COSMIC: COSV74141017;