6-32701069-G-T

Variant names:

• chr6-32701069-G-T
• rs9275383

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 0.109 in 152,062 control chromosomes in the GnomAD database, including 1,040 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 0.11 (1040 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.78
• Publications: 17 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.179 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: 0.109 AC: 16545 AN: 151944 Hom.: 1039 Cov.: 31

Gnomad AFR AF: 0.0669

Gnomad AMI AF: 0.142

Gnomad AMR AF: 0.185

Gnomad ASJ AF: 0.173

Gnomad EAS AF: 0.162

Gnomad SAS AF: 0.105

Gnomad FIN AF: 0.144

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.105

Gnomad OTH AF: 0.102

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

GnomAD4 genome AF: 0.109 AC: 16560 AN: 152062 Hom.: 1040 Cov.: 31 AF XY: 0.112 AC XY: 8356 AN XY: 74316

African (AFR) AF: 0.0669 AC: 2775 AN: 41478

American (AMR) AF: 0.185 AC: 2830 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.173 AC: 599 AN: 3466

East Asian (EAS) AF: 0.162 AC: 838 AN: 5158

South Asian (SAS) AF: 0.105 AC: 505 AN: 4816

European-Finnish (FIN) AF: 0.144 AC: 1514 AN: 10542

Middle Eastern (MID) AF: 0.102 AC: 30 AN: 294

European-Non Finnish (NFE) AF: 0.105 AC: 7126 AN: 67998

Other (OTH) AF: 0.101 AC: 214 AN: 2114

Alfa AF: 0.0955 Hom.: 440

Bravo AF: 0.114

Asia WGS AF: 0.123 AC: 429 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.8
DANN	Benign	0.43
PhyloP100		-2.8

Splicing

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

Other links and lift over

dbSNP: rs9275383; hg19: chr6-32668846;