rs1343232

Variant names:

• chr6-81420615-A-G
• rs1343232

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.320 AC: 13286 AN: 41506

American (AMR) AF: 0.418 AC: 6376 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.322 AC: 1117 AN: 3472

East Asian (EAS) AF: 0.328 AC: 1694 AN: 5168

South Asian (SAS) AF: 0.289 AC: 1396 AN: 4824

European-Finnish (FIN) AF: 0.403 AC: 4263 AN: 10576

Middle Eastern (MID) AF: 0.327 AC: 96 AN: 294

European-Non Finnish (NFE) AF: 0.421 AC: 28571 AN: 67934

Other (OTH) AF: 0.353 AC: 745 AN: 2112

Alfa AF: 0.404 Hom.: 10237

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
PhyloP100		0.93

Splicing

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

Other links and lift over

dbSNP: rs1343232; hg19: chr6-82130332;