6-32704358-C-T

Variant names:

• chr6-32704358-C-T
• rs17499655

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 0.182 in 143,522 control chromosomes in the GnomAD database, including 2,765 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 0.18 (2765 hom., cov: 27)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.991
• Publications: 15 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.22 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: 0.182 AC: 26111 AN: 143412 Hom.: 2758 Cov.: 27

Gnomad AFR AF: 0.224

Gnomad AMI AF: 0.257

Gnomad AMR AF: 0.207

Gnomad ASJ AF: 0.151

Gnomad EAS AF: 0.136

Gnomad SAS AF: 0.0997

Gnomad FIN AF: 0.327

Gnomad MID AF: 0.103

Gnomad NFE AF: 0.143

Gnomad OTH AF: 0.185

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

GnomAD4 genome AF: 0.182 AC: 26152 AN: 143522 Hom.: 2765 Cov.: 27 AF XY: 0.188 AC XY: 13044 AN XY: 69484

African (AFR) AF: 0.224 AC: 8657 AN: 38618

American (AMR) AF: 0.207 AC: 2964 AN: 14308

Ashkenazi Jewish (ASJ) AF: 0.151 AC: 516 AN: 3406

East Asian (EAS) AF: 0.136 AC: 650 AN: 4790

South Asian (SAS) AF: 0.102 AC: 461 AN: 4534

European-Finnish (FIN) AF: 0.327 AC: 2845 AN: 8696

Middle Eastern (MID) AF: 0.107 AC: 29 AN: 270

European-Non Finnish (NFE) AF: 0.143 AC: 9431 AN: 65994

Other (OTH) AF: 0.184 AC: 372 AN: 2024

Alfa AF: 0.158 Hom.: 3807

Bravo AF: 0.182

Asia WGS AF: 0.153 AC: 537 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	5.5
DANN	Benign	0.46
PhyloP100		-0.99

Splicing

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

Other links and lift over

dbSNP: rs17499655; hg19: chr6-32672135;