6-32713578-T-C

Variant names:

• chr6-32713578-T-C
• rs9275595

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 0.226 in 152,118 control chromosomes in the GnomAD database, including 4,093 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 0.23 (4093 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.125
• Publications: 34 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.289 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: 0.226 AC: 34337 AN: 152002 Hom.: 4085 Cov.: 32

Gnomad AFR AF: 0.191

Gnomad AMI AF: 0.364

Gnomad AMR AF: 0.296

Gnomad ASJ AF: 0.303

Gnomad EAS AF: 0.221

Gnomad SAS AF: 0.160

Gnomad FIN AF: 0.318

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.216

Gnomad OTH AF: 0.234

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

GnomAD4 genome AF: 0.226 AC: 34384 AN: 152118 Hom.: 4093 Cov.: 32 AF XY: 0.231 AC XY: 17141 AN XY: 74362

African (AFR) AF: 0.192 AC: 7952 AN: 41494

American (AMR) AF: 0.296 AC: 4531 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.303 AC: 1051 AN: 3472

East Asian (EAS) AF: 0.221 AC: 1143 AN: 5172

South Asian (SAS) AF: 0.162 AC: 780 AN: 4826

European-Finnish (FIN) AF: 0.318 AC: 3369 AN: 10580

Middle Eastern (MID) AF: 0.163 AC: 48 AN: 294

European-Non Finnish (NFE) AF: 0.216 AC: 14689 AN: 67964

Other (OTH) AF: 0.231 AC: 489 AN: 2114

Alfa AF: 0.220 Hom.: 10148

Bravo AF: 0.227

Asia WGS AF: 0.179 AC: 628 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.5
DANN	Benign	0.51
PhyloP100		0.13

Splicing

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

Other links and lift over

dbSNP: rs9275595; hg19: chr6-32681355;