rs432695

chr6-4674478-A-G

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 0.18 in 151,938 control chromosomes in the GnomAD database, including 2,523 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 0.18 (2523 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.43

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.194 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: 0.180 AC: 27280 AN: 151820 Hom.: 2512 Cov.: 30

Gnomad AFR AF: 0.139

Gnomad AMI AF: 0.0932

Gnomad AMR AF: 0.199

Gnomad ASJ AF: 0.192

Gnomad EAS AF: 0.121

Gnomad SAS AF: 0.200

Gnomad FIN AF: 0.223

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.197

Gnomad OTH AF: 0.177

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

GnomAD4 genome AF: 0.180 AC: 27327 AN: 151938 Hom.: 2523 Cov.: 30 AF XY: 0.180 AC XY: 13365 AN XY: 74262

Gnomad4 AFR AF: 0.140

Gnomad4 AMR AF: 0.200

Gnomad4 ASJ AF: 0.192

Gnomad4 EAS AF: 0.121

Gnomad4 SAS AF: 0.202

Gnomad4 FIN AF: 0.223

Gnomad4 NFE AF: 0.197

Gnomad4 OTH AF: 0.178

Alfa AF: 0.194 Hom.: 3977

Bravo AF: 0.174

Asia WGS AF: 0.181 AC: 630 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	0.42
Dann	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs432695; hg19: chr6-4674712;