rs1205035

chr6-3485197-C-T

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 0.55 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.730

Gnomad4 AMR AF: 0.612

Gnomad4 ASJ AF: 0.470

Gnomad4 EAS AF: 0.494

Gnomad4 SAS AF: 0.384

Gnomad4 FIN AF: 0.393

Gnomad4 NFE AF: 0.469

Gnomad4 OTH AF: 0.565

Alfa AF: 0.527 Hom.: 3692

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1205035; hg19: chr6-3485431;