rs1343232

Positions:

• chr6-81420615-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 0.381 in 152,044 control chromosomes in the GnomAD database, including 11,287 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 0.38 (11287 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.932

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 (NFE) allele frequency at 95% confidence interval = 0.416 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: 0.381 AC: 57933 AN: 151926 Hom.: 11293 Cov.: 32

Gnomad AFR AF: 0.321

Gnomad AMI AF: 0.430

Gnomad AMR AF: 0.419

Gnomad ASJ AF: 0.322

Gnomad EAS AF: 0.328

Gnomad SAS AF: 0.289

Gnomad FIN AF: 0.403

Gnomad MID AF: 0.329

Gnomad NFE AF: 0.421

Gnomad OTH AF: 0.357

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

GnomAD4 genome AF: 0.381 AC: 57935 AN: 152044 Hom.: 11287 Cov.: 32 AF XY: 0.380 AC XY: 28244 AN XY: 74324

Gnomad4 AFR AF: 0.320

Gnomad4 AMR AF: 0.418

Gnomad4 ASJ AF: 0.322

Gnomad4 EAS AF: 0.328

Gnomad4 SAS AF: 0.289

Gnomad4 FIN AF: 0.403

Gnomad4 NFE AF: 0.421

Gnomad4 OTH AF: 0.353

Alfa AF: 0.400 Hom.: 6992

Bravo AF: 0.382

Asia WGS AF: 0.295 AC: 1027 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.1
DANN	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1343232; hg19: chr6-82130332;