rs283545

Variant names:

• chr6-51000259-C-T
• rs283545

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 0.502 in 151,940 control chromosomes in the GnomAD database, including 19,412 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 0.50 (19412 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.440
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.566 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: 0.503 AC: 76290 AN: 151820 Hom.: 19397 Cov.: 32

Gnomad AFR AF: 0.572

Gnomad AMI AF: 0.297

Gnomad AMR AF: 0.503

Gnomad ASJ AF: 0.406

Gnomad EAS AF: 0.373

Gnomad SAS AF: 0.475

Gnomad FIN AF: 0.519

Gnomad MID AF: 0.414

Gnomad NFE AF: 0.479

Gnomad OTH AF: 0.466

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

GnomAD4 genome AF: 0.502 AC: 76348 AN: 151940 Hom.: 19412 Cov.: 32 AF XY: 0.502 AC XY: 37243 AN XY: 74240

African (AFR) AF: 0.572 AC: 23702 AN: 41464

American (AMR) AF: 0.503 AC: 7666 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.406 AC: 1407 AN: 3468

East Asian (EAS) AF: 0.373 AC: 1925 AN: 5164

South Asian (SAS) AF: 0.476 AC: 2291 AN: 4818

European-Finnish (FIN) AF: 0.519 AC: 5465 AN: 10524

Middle Eastern (MID) AF: 0.425 AC: 124 AN: 292

European-Non Finnish (NFE) AF: 0.479 AC: 32520 AN: 67944

Other (OTH) AF: 0.463 AC: 977 AN: 2108

Alfa AF: 0.506 Hom.: 2570

Bravo AF: 0.504

Asia WGS AF: 0.488 AC: 1697 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.5
DANN	Benign	0.50
PhyloP100		0.44

Splicing

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

Other links and lift over

dbSNP: rs283545; hg19: chr6-50967972;