6-132641914-T-C

Variant names:

• chr6-132641914-T-C
• rs9389020

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 0.255 in 152,032 control chromosomes in the GnomAD database, including 5,296 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 (5296 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.742
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.431 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: 0.255 AC: 38751 AN: 151914 Hom.: 5286 Cov.: 32

Gnomad AFR AF: 0.183

Gnomad AMI AF: 0.229

Gnomad AMR AF: 0.239

Gnomad ASJ AF: 0.182

Gnomad EAS AF: 0.447

Gnomad SAS AF: 0.318

Gnomad FIN AF: 0.293

Gnomad MID AF: 0.225

Gnomad NFE AF: 0.283

Gnomad OTH AF: 0.227

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

GnomAD4 genome AF: 0.255 AC: 38784 AN: 152032 Hom.: 5296 Cov.: 32 AF XY: 0.259 AC XY: 19237 AN XY: 74306

African (AFR) AF: 0.183 AC: 7616 AN: 41516

American (AMR) AF: 0.238 AC: 3632 AN: 15234

Ashkenazi Jewish (ASJ) AF: 0.182 AC: 632 AN: 3468

East Asian (EAS) AF: 0.446 AC: 2303 AN: 5166

South Asian (SAS) AF: 0.319 AC: 1538 AN: 4828

European-Finnish (FIN) AF: 0.293 AC: 3108 AN: 10596

Middle Eastern (MID) AF: 0.207 AC: 61 AN: 294

European-Non Finnish (NFE) AF: 0.283 AC: 19194 AN: 67908

Other (OTH) AF: 0.233 AC: 491 AN: 2110

Alfa AF: 0.271 Hom.: 17980

Bravo AF: 0.247

Asia WGS AF: 0.364 AC: 1263 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.2
DANN	Benign	0.76
PhyloP100		-0.74

Splicing

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

Other links and lift over

dbSNP: rs9389020; hg19: chr6-132963053;