6-32703744-T-C

Variant names:

• chr6-32703744-T-C
• rs9275439

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 0.295 in 151,760 control chromosomes in the GnomAD database, including 7,038 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 0.29 (7038 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.158
• Publications: 36 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.389 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: 0.295 AC: 44704 AN: 151642 Hom.: 7022 Cov.: 30

Gnomad AFR AF: 0.294

Gnomad AMI AF: 0.400

Gnomad AMR AF: 0.397

Gnomad ASJ AF: 0.326

Gnomad EAS AF: 0.295

Gnomad SAS AF: 0.210

Gnomad FIN AF: 0.467

Gnomad MID AF: 0.204

Gnomad NFE AF: 0.249

Gnomad OTH AF: 0.291

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

GnomAD4 genome AF: 0.295 AC: 44765 AN: 151760 Hom.: 7038 Cov.: 30 AF XY: 0.305 AC XY: 22604 AN XY: 74154

African (AFR) AF: 0.294 AC: 12156 AN: 41374

American (AMR) AF: 0.398 AC: 6062 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.326 AC: 1128 AN: 3464

East Asian (EAS) AF: 0.295 AC: 1517 AN: 5134

South Asian (SAS) AF: 0.212 AC: 1019 AN: 4808

European-Finnish (FIN) AF: 0.467 AC: 4896 AN: 10478

Middle Eastern (MID) AF: 0.209 AC: 61 AN: 292

European-Non Finnish (NFE) AF: 0.250 AC: 16952 AN: 67942

Other (OTH) AF: 0.288 AC: 609 AN: 2114

Alfa AF: 0.280 Hom.: 14293

Bravo AF: 0.295

Asia WGS AF: 0.277 AC: 968 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	5.9
DANN	Benign	0.66
PhyloP100		-0.16

Splicing

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

Other links and lift over

dbSNP: rs9275439; hg19: chr6-32671521;