10-42558904-T-C

Variant names:

• chr10-42558904-T-C
• rs68055

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 0.777 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.777 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

Gnomad4 AFR AF: 0.634

Gnomad4 AMR AF: 0.824

Gnomad4 ASJ AF: 0.783

Gnomad4 EAS AF: 0.963

Gnomad4 SAS AF: 0.774

Gnomad4 FIN AF: 0.725

Gnomad4 NFE AF: 0.847

Gnomad4 OTH AF: 0.796

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

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