6-104058829-C-T

Variant names:

• chr6-104058829-C-T
• rs1648957

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 0.386 in 151,926 control chromosomes in the GnomAD database, including 13,323 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 0.39 (13323 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.277
• Publications: 0 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.563 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: 0.386 AC: 58636 AN: 151808 Hom.: 13311 Cov.: 31

Gnomad AFR AF: 0.144

Gnomad AMI AF: 0.349

Gnomad AMR AF: 0.572

Gnomad ASJ AF: 0.482

Gnomad EAS AF: 0.523

Gnomad SAS AF: 0.378

Gnomad FIN AF: 0.444

Gnomad MID AF: 0.459

Gnomad NFE AF: 0.467

Gnomad OTH AF: 0.434

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

GnomAD4 genome AF: 0.386 AC: 58669 AN: 151926 Hom.: 13323 Cov.: 31 AF XY: 0.389 AC XY: 28866 AN XY: 74242

African (AFR) AF: 0.144 AC: 5975 AN: 41458

American (AMR) AF: 0.573 AC: 8732 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.482 AC: 1674 AN: 3472

East Asian (EAS) AF: 0.524 AC: 2699 AN: 5154

South Asian (SAS) AF: 0.379 AC: 1827 AN: 4822

European-Finnish (FIN) AF: 0.444 AC: 4677 AN: 10540

Middle Eastern (MID) AF: 0.463 AC: 136 AN: 294

European-Non Finnish (NFE) AF: 0.467 AC: 31715 AN: 67930

Other (OTH) AF: 0.435 AC: 916 AN: 2108

Alfa AF: 0.348 Hom.: 1583

Bravo AF: 0.390

Asia WGS AF: 0.427 AC: 1487 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	2.6
DANN	Benign	0.74
PhyloP100		-0.28

Splicing

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

Other links and lift over

dbSNP: rs1648957; hg19: chr6-104506704;