chr10-5994181-T-C

Variant names:

• chr10-5994181-T-C
• rs4749882

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 0.668 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
• Publications: 7 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.618 AC: 25593 AN: 41446

American (AMR) AF: 0.715 AC: 10930 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.720 AC: 2501 AN: 3472

East Asian (EAS) AF: 0.600 AC: 3099 AN: 5166

South Asian (SAS) AF: 0.662 AC: 3190 AN: 4818

European-Finnish (FIN) AF: 0.662 AC: 6987 AN: 10560

Middle Eastern (MID) AF: 0.805 AC: 235 AN: 292

European-Non Finnish (NFE) AF: 0.691 AC: 46948 AN: 67968

Other (OTH) AF: 0.705 AC: 1491 AN: 2114

Alfa AF: 0.693 Hom.: 65619

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
PhyloP100		-0.71

Splicing

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

Other links and lift over

dbSNP: rs4749882; hg19: chr10-6036144;