10-5994181-T-C

Variant names:

• chr10-5994181-T-C
• rs4749882

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 0.668 in 152,034 control chromosomes in the GnomAD database, including 34,156 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 0.67 (34156 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.708

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.704 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: 0.668 AC: 101524 AN: 151916 Hom.: 34132 Cov.: 32

Gnomad AFR AF: 0.618

Gnomad AMI AF: 0.677

Gnomad AMR AF: 0.715

Gnomad ASJ AF: 0.720

Gnomad EAS AF: 0.598

Gnomad SAS AF: 0.660

Gnomad FIN AF: 0.662

Gnomad MID AF: 0.799

Gnomad NFE AF: 0.691

Gnomad OTH AF: 0.708

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

GnomAD4 genome AF: 0.668 AC: 101591 AN: 152034 Hom.: 34156 Cov.: 32 AF XY: 0.667 AC XY: 49558 AN XY: 74326

Gnomad4 AFR AF: 0.618

Gnomad4 AMR AF: 0.715

Gnomad4 ASJ AF: 0.720

Gnomad4 EAS AF: 0.600

Gnomad4 SAS AF: 0.662

Gnomad4 FIN AF: 0.662

Gnomad4 NFE AF: 0.691

Gnomad4 OTH AF: 0.705

Alfa AF: 0.697 Hom.: 47396

Bravo AF: 0.676

Asia WGS AF: 0.583 AC: 2028 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	2.2
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4749882; hg19: chr10-6036144;