6-32411518-G-C

Variant names:

• chr6-32411518-G-C
• rs9268515

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 0.16 in 113,414 control chromosomes in the GnomAD database, including 1,415 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 0.16 (1415 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.797
• Publications: 18 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.201 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: 0.160 AC: 18120 AN: 113322 Hom.: 1416 Cov.: 29

Gnomad AFR AF: 0.0513

Gnomad AMI AF: 0.221

Gnomad AMR AF: 0.204

Gnomad ASJ AF: 0.0751

Gnomad EAS AF: 0.108

Gnomad SAS AF: 0.127

Gnomad FIN AF: 0.195

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.204

Gnomad OTH AF: 0.119

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

GnomAD4 genome AF: 0.160 AC: 18127 AN: 113414 Hom.: 1415 Cov.: 29 AF XY: 0.158 AC XY: 8697 AN XY: 55028

African (AFR) AF: 0.0511 AC: 1325 AN: 25930

American (AMR) AF: 0.205 AC: 2394 AN: 11692

Ashkenazi Jewish (ASJ) AF: 0.0751 AC: 176 AN: 2344

East Asian (EAS) AF: 0.108 AC: 354 AN: 3278

South Asian (SAS) AF: 0.128 AC: 409 AN: 3196

European-Finnish (FIN) AF: 0.195 AC: 1542 AN: 7924

Middle Eastern (MID) AF: 0.110 AC: 24 AN: 218

European-Non Finnish (NFE) AF: 0.204 AC: 11591 AN: 56734

Other (OTH) AF: 0.117 AC: 169 AN: 1450

Alfa AF: 0.0753 Hom.: 107

Bravo AF: 0.120

Asia WGS AF: 0.0710 AC: 250 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.29
DANN	Benign	0.36
PhyloP100		-0.80

Splicing

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

Other links and lift over

dbSNP: rs9268515; hg19: chr6-32379295;