chr6-32681887-T-C

Variant names:

• chr6-32681887-T-C
• rs1694112

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 0.259 in 152,078 control chromosomes in the GnomAD database, including 5,391 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 0.26 (5391 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.02
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.428 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: 0.259 AC: 39358 AN: 151958 Hom.: 5397 Cov.: 32

Gnomad AFR AF: 0.263

Gnomad AMI AF: 0.312

Gnomad AMR AF: 0.241

Gnomad ASJ AF: 0.293

Gnomad EAS AF: 0.444

Gnomad SAS AF: 0.243

Gnomad FIN AF: 0.183

Gnomad MID AF: 0.392

Gnomad NFE AF: 0.256

Gnomad OTH AF: 0.271

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

GnomAD4 genome AF: 0.259 AC: 39369 AN: 152078 Hom.: 5391 Cov.: 32 AF XY: 0.255 AC XY: 19000 AN XY: 74376

African (AFR) AF: 0.262 AC: 10883 AN: 41476

American (AMR) AF: 0.241 AC: 3680 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.293 AC: 1016 AN: 3472

East Asian (EAS) AF: 0.443 AC: 2293 AN: 5178

South Asian (SAS) AF: 0.241 AC: 1158 AN: 4808

European-Finnish (FIN) AF: 0.183 AC: 1939 AN: 10570

Middle Eastern (MID) AF: 0.391 AC: 115 AN: 294

European-Non Finnish (NFE) AF: 0.256 AC: 17419 AN: 67982

Other (OTH) AF: 0.276 AC: 582 AN: 2112

Alfa AF: 0.245 Hom.: 2358

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.10
DANN	Benign	0.52
PhyloP100		-2.0

Splicing

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

Other links and lift over

dbSNP: rs1694112; hg19: chr6-32649664;