rs1205035

Variant names:

• chr6-3485197-C-T
• rs1205035

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 0.55 in 152,004 control chromosomes in the GnomAD database, including 24,182 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 0.55 (24182 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.742
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.724 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: 0.549 AC: 83424 AN: 151886 Hom.: 24125 Cov.: 32

Gnomad AFR AF: 0.730

Gnomad AMI AF: 0.537

Gnomad AMR AF: 0.612

Gnomad ASJ AF: 0.470

Gnomad EAS AF: 0.495

Gnomad SAS AF: 0.385

Gnomad FIN AF: 0.393

Gnomad MID AF: 0.525

Gnomad NFE AF: 0.469

Gnomad OTH AF: 0.560

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

GnomAD4 genome AF: 0.550 AC: 83542 AN: 152004 Hom.: 24182 Cov.: 32 AF XY: 0.545 AC XY: 40512 AN XY: 74284

African (AFR) AF: 0.730 AC: 30285 AN: 41462

American (AMR) AF: 0.612 AC: 9362 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.470 AC: 1631 AN: 3472

East Asian (EAS) AF: 0.494 AC: 2549 AN: 5156

South Asian (SAS) AF: 0.384 AC: 1852 AN: 4818

European-Finnish (FIN) AF: 0.393 AC: 4141 AN: 10540

Middle Eastern (MID) AF: 0.520 AC: 153 AN: 294

European-Non Finnish (NFE) AF: 0.469 AC: 31885 AN: 67950

Other (OTH) AF: 0.565 AC: 1195 AN: 2114

Alfa AF: 0.532 Hom.: 3894

Bravo AF: 0.579

Asia WGS AF: 0.472 AC: 1643 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	2.0
DANN	Benign	0.87
PhyloP100		-0.74

Splicing

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

Other links and lift over

dbSNP: rs1205035; hg19: chr6-3485431;