rs2395175

Positions:

• chr6-32437249-G-A

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 0.119 in 152,178 control chromosomes in the GnomAD database, including 1,294 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 0.12 (1294 hom., cov: 31)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.325

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.156 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.32437249G>A		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.119 AC: 18086 AN: 152060 Hom.: 1295 Cov.: 31

Gnomad AFR AF: 0.0601

Gnomad AMI AF: 0.158

Gnomad AMR AF: 0.141

Gnomad ASJ AF: 0.0378

Gnomad EAS AF: 0.0668

Gnomad SAS AF: 0.0803

Gnomad FIN AF: 0.137

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.159

Gnomad OTH AF: 0.0813

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

GnomAD4 genome AF: 0.119 AC: 18094 AN: 152178 Hom.: 1294 Cov.: 31 AF XY: 0.116 AC XY: 8632 AN XY: 74396

Gnomad4 AFR AF: 0.0600

Gnomad4 AMR AF: 0.141

Gnomad4 ASJ AF: 0.0378

Gnomad4 EAS AF: 0.0672

Gnomad4 SAS AF: 0.0808

Gnomad4 FIN AF: 0.137

Gnomad4 NFE AF: 0.159

Gnomad4 OTH AF: 0.0800

Alfa AF: 0.144 Hom.: 2220

Bravo AF: 0.120

Asia WGS AF: 0.0680 AC: 240 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	8.9
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2395175; hg19: chr6-32405026; COSMIC: COSV66622731;