rs2395228

Positions:

• chr6-32655446-A-C
• chr6-32655446-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 0.115 in 124,078 control chromosomes in the GnomAD database, including 846 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 (846 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.766

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.146 is higher than 0.05.

Transcripts

RefSeq

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

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.116 AC: 14320 AN: 123982 Hom.: 845 Cov.: 29

Gnomad AFR AF: 0.0834

Gnomad AMI AF: 0.0667

Gnomad AMR AF: 0.0837

Gnomad ASJ AF: 0.0762

Gnomad EAS AF: 0.0597

Gnomad SAS AF: 0.138

Gnomad FIN AF: 0.0990

Gnomad MID AF: 0.154

Gnomad NFE AF: 0.149

Gnomad OTH AF: 0.112

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

GnomAD4 genome AF: 0.115 AC: 14327 AN: 124078 Hom.: 846 Cov.: 29 AF XY: 0.113 AC XY: 6811 AN XY: 60454

Gnomad4 AFR AF: 0.0833

Gnomad4 AMR AF: 0.0836

Gnomad4 ASJ AF: 0.0762

Gnomad4 EAS AF: 0.0597

Gnomad4 SAS AF: 0.139

Gnomad4 FIN AF: 0.0990

Gnomad4 NFE AF: 0.149

Gnomad4 OTH AF: 0.111

Alfa AF: 0.103 Hom.: 757

Bravo AF: 0.0916

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	5.1
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2395228; hg19: chr6-32623223;