rs6451692

Variant names:

• chr5-43433633-G-C
• rs6451692

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 0.582 in 151,926 control chromosomes in the GnomAD database, including 27,405 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 0.58 (27405 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.367
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.779 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: 0.582 AC: 88294 AN: 151808 Hom.: 27371 Cov.: 31

Gnomad AFR AF: 0.786

Gnomad AMI AF: 0.593

Gnomad AMR AF: 0.464

Gnomad ASJ AF: 0.598

Gnomad EAS AF: 0.221

Gnomad SAS AF: 0.427

Gnomad FIN AF: 0.483

Gnomad MID AF: 0.725

Gnomad NFE AF: 0.535

Gnomad OTH AF: 0.598

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

GnomAD4 genome AF: 0.582 AC: 88373 AN: 151926 Hom.: 27405 Cov.: 31 AF XY: 0.572 AC XY: 42486 AN XY: 74232

African (AFR) AF: 0.786 AC: 32591 AN: 41464

American (AMR) AF: 0.463 AC: 7067 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.598 AC: 2072 AN: 3466

East Asian (EAS) AF: 0.221 AC: 1142 AN: 5160

South Asian (SAS) AF: 0.425 AC: 2040 AN: 4800

European-Finnish (FIN) AF: 0.483 AC: 5081 AN: 10526

Middle Eastern (MID) AF: 0.718 AC: 211 AN: 294

European-Non Finnish (NFE) AF: 0.535 AC: 36369 AN: 67942

Other (OTH) AF: 0.599 AC: 1263 AN: 2110

Alfa AF: 0.556 Hom.: 3015

Bravo AF: 0.591

Asia WGS AF: 0.387 AC: 1346 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.81
DANN	Benign	0.41
PhyloP100		-0.37

Splicing

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

Other links and lift over

dbSNP: rs6451692; hg19: chr5-43433735; COSMIC: COSV59181410;