6-32231367-C-A

Variant names:

• chr6-32231367-C-A
• rs377763

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 0.202 in 152,128 control chromosomes in the GnomAD database, including 3,237 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 0.20 (3237 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.579
• Publications: 44 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.271 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: 0.202 AC: 30753 AN: 152010 Hom.: 3236 Cov.: 32

Gnomad AFR AF: 0.212

Gnomad AMI AF: 0.109

Gnomad AMR AF: 0.161

Gnomad ASJ AF: 0.259

Gnomad EAS AF: 0.163

Gnomad SAS AF: 0.284

Gnomad FIN AF: 0.166

Gnomad MID AF: 0.212

Gnomad NFE AF: 0.206

Gnomad OTH AF: 0.230

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

GnomAD4 genome AF: 0.202 AC: 30755 AN: 152128 Hom.: 3237 Cov.: 32 AF XY: 0.200 AC XY: 14855 AN XY: 74360

African (AFR) AF: 0.211 AC: 8769 AN: 41502

American (AMR) AF: 0.161 AC: 2457 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.259 AC: 900 AN: 3472

East Asian (EAS) AF: 0.163 AC: 839 AN: 5160

South Asian (SAS) AF: 0.283 AC: 1367 AN: 4824

European-Finnish (FIN) AF: 0.166 AC: 1756 AN: 10588

Middle Eastern (MID) AF: 0.211 AC: 62 AN: 294

European-Non Finnish (NFE) AF: 0.206 AC: 14020 AN: 67984

Other (OTH) AF: 0.230 AC: 486 AN: 2112

Alfa AF: 0.208 Hom.: 10209

Bravo AF: 0.203

Asia WGS AF: 0.259 AC: 904 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.86
DANN	Benign	0.43
PhyloP100		-0.58

Splicing

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

Other links and lift over

dbSNP: rs377763; hg19: chr6-32199144;