rs3132506

chr6-31208449-T-Cchr6-31208449-T-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 0.241 in 152,142 control chromosomes in the GnomAD database, including 4,479 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 0.24 (4479 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.168

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.259 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: 0.241 AC: 36660 AN: 152024 Hom.: 4473 Cov.: 32

Gnomad AFR AF: 0.263

Gnomad AMI AF: 0.345

Gnomad AMR AF: 0.204

Gnomad ASJ AF: 0.281

Gnomad EAS AF: 0.209

Gnomad SAS AF: 0.150

Gnomad FIN AF: 0.166

Gnomad MID AF: 0.256

Gnomad NFE AF: 0.253

Gnomad OTH AF: 0.246

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

GnomAD4 genome AF: 0.241 AC: 36683 AN: 152142 Hom.: 4479 Cov.: 32 AF XY: 0.233 AC XY: 17365 AN XY: 74390

Gnomad4 AFR AF: 0.263

Gnomad4 AMR AF: 0.204

Gnomad4 ASJ AF: 0.281

Gnomad4 EAS AF: 0.209

Gnomad4 SAS AF: 0.149

Gnomad4 FIN AF: 0.166

Gnomad4 NFE AF: 0.253

Gnomad4 OTH AF: 0.246

Alfa AF: 0.251 Hom.: 6723

Bravo AF: 0.245

Asia WGS AF: 0.156 AC: 546 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	5.8
Dann	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3132506; hg19: chr6-31176226;