rs10042968

Variant names:

• chr5-63737891-A-G
• rs10042968

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 0.202 in 152,052 control chromosomes in the GnomAD database, including 3,308 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 0.20 (3308 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.65

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.238 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: 0.202 AC: 30682 AN: 151934 Hom.: 3307 Cov.: 33

Gnomad AFR AF: 0.242

Gnomad AMI AF: 0.239

Gnomad AMR AF: 0.175

Gnomad ASJ AF: 0.209

Gnomad EAS AF: 0.0226

Gnomad SAS AF: 0.102

Gnomad FIN AF: 0.158

Gnomad MID AF: 0.247

Gnomad NFE AF: 0.210

Gnomad OTH AF: 0.205

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

GnomAD4 genome AF: 0.202 AC: 30695 AN: 152052 Hom.: 3308 Cov.: 33 AF XY: 0.197 AC XY: 14670 AN XY: 74344

Gnomad4 AFR AF: 0.241

Gnomad4 AMR AF: 0.175

Gnomad4 ASJ AF: 0.209

Gnomad4 EAS AF: 0.0227

Gnomad4 SAS AF: 0.103

Gnomad4 FIN AF: 0.158

Gnomad4 NFE AF: 0.210

Gnomad4 OTH AF: 0.203

Alfa AF: 0.208 Hom.: 648

Bravo AF: 0.207

Asia WGS AF: 0.0720 AC: 253 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	16
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10042968; hg19: chr5-63033718;