10-6077003-C-T

Variant names:

• chr10-6077003-C-T
• rs4749955

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 0.442 in 151,922 control chromosomes in the GnomAD database, including 16,846 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 0.44 (16846 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.832
• Publications: 18 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 (NFE) allele frequency at 95% confidence interval = 0.557 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: 0.443 AC: 67176 AN: 151804 Hom.: 16833 Cov.: 30

Gnomad AFR AF: 0.215

Gnomad AMI AF: 0.524

Gnomad AMR AF: 0.453

Gnomad ASJ AF: 0.578

Gnomad EAS AF: 0.289

Gnomad SAS AF: 0.522

Gnomad FIN AF: 0.522

Gnomad MID AF: 0.576

Gnomad NFE AF: 0.562

Gnomad OTH AF: 0.488

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

GnomAD4 genome AF: 0.442 AC: 67201 AN: 151922 Hom.: 16846 Cov.: 30 AF XY: 0.440 AC XY: 32632 AN XY: 74224

African (AFR) AF: 0.215 AC: 8915 AN: 41438

American (AMR) AF: 0.452 AC: 6909 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.578 AC: 2005 AN: 3466

East Asian (EAS) AF: 0.288 AC: 1488 AN: 5158

South Asian (SAS) AF: 0.524 AC: 2515 AN: 4798

European-Finnish (FIN) AF: 0.522 AC: 5500 AN: 10530

Middle Eastern (MID) AF: 0.592 AC: 173 AN: 292

European-Non Finnish (NFE) AF: 0.562 AC: 38182 AN: 67950

Other (OTH) AF: 0.492 AC: 1036 AN: 2106

Alfa AF: 0.526 Hom.: 91975

Bravo AF: 0.423

Asia WGS AF: 0.409 AC: 1426 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.39
DANN	Benign	0.48
PhyloP100		-0.83

Splicing

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

Other links and lift over

dbSNP: rs4749955; hg19: chr10-6118966;