6-32240547-C-T

Variant names:

• chr6-32240547-C-T
• rs424232

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 0.302 in 151,978 control chromosomes in the GnomAD database, including 7,286 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 0.30 (7286 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.270
• Publications: 50 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.366 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: 0.302 AC: 45911 AN: 151860 Hom.: 7284 Cov.: 31

Gnomad AFR AF: 0.308

Gnomad AMI AF: 0.215

Gnomad AMR AF: 0.292

Gnomad ASJ AF: 0.524

Gnomad EAS AF: 0.345

Gnomad SAS AF: 0.381

Gnomad FIN AF: 0.166

Gnomad MID AF: 0.481

Gnomad NFE AF: 0.301

Gnomad OTH AF: 0.347

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

GnomAD4 genome AF: 0.302 AC: 45931 AN: 151978 Hom.: 7286 Cov.: 31 AF XY: 0.297 AC XY: 22083 AN XY: 74282

African (AFR) AF: 0.308 AC: 12746 AN: 41410

American (AMR) AF: 0.292 AC: 4464 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.524 AC: 1816 AN: 3466

East Asian (EAS) AF: 0.345 AC: 1782 AN: 5164

South Asian (SAS) AF: 0.381 AC: 1835 AN: 4820

European-Finnish (FIN) AF: 0.166 AC: 1752 AN: 10562

Middle Eastern (MID) AF: 0.483 AC: 142 AN: 294

European-Non Finnish (NFE) AF: 0.301 AC: 20467 AN: 67960

Other (OTH) AF: 0.346 AC: 731 AN: 2114

Alfa AF: 0.312 Hom.: 27468

Bravo AF: 0.309

Asia WGS AF: 0.346 AC: 1208 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	12
DANN	Benign	0.54
PhyloP100		-0.27

Splicing

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

Other links and lift over

dbSNP: rs424232; hg19: chr6-32208324;