rs6451692

chr5-43433633-G-C

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 0.582 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.786

Gnomad4 AMR AF: 0.463

Gnomad4 ASJ AF: 0.598

Gnomad4 EAS AF: 0.221

Gnomad4 SAS AF: 0.425

Gnomad4 FIN AF: 0.483

Gnomad4 NFE AF: 0.535

Gnomad4 OTH AF: 0.599

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

Splicing

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

Publications

LitVar

Other links and lift over

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