6-32716610-A-G

Variant names:

• chr6-32716610-A-G
• rs9275618

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 0.131 in 152,110 control chromosomes in the GnomAD database, including 1,379 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 0.13 (1379 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.816
• Publications: 15 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.7).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.176 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: 0.131 AC: 19912 AN: 151992 Hom.: 1373 Cov.: 32

Gnomad AFR AF: 0.162

Gnomad AMI AF: 0.110

Gnomad AMR AF: 0.123

Gnomad ASJ AF: 0.143

Gnomad EAS AF: 0.185

Gnomad SAS AF: 0.0764

Gnomad FIN AF: 0.139

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.113

Gnomad OTH AF: 0.109

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

GnomAD4 genome AF: 0.131 AC: 19950 AN: 152110 Hom.: 1379 Cov.: 32 AF XY: 0.131 AC XY: 9761 AN XY: 74352

African (AFR) AF: 0.163 AC: 6751 AN: 41474

American (AMR) AF: 0.123 AC: 1878 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.143 AC: 495 AN: 3464

East Asian (EAS) AF: 0.186 AC: 958 AN: 5164

South Asian (SAS) AF: 0.0763 AC: 367 AN: 4810

European-Finnish (FIN) AF: 0.139 AC: 1471 AN: 10582

Middle Eastern (MID) AF: 0.0986 AC: 29 AN: 294

European-Non Finnish (NFE) AF: 0.113 AC: 7673 AN: 68004

Other (OTH) AF: 0.108 AC: 228 AN: 2116

Alfa AF: 0.132 Hom.: 720

Bravo AF: 0.134

Asia WGS AF: 0.111 AC: 386 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.70
CADD	Benign	15
DANN	Benign	0.94
PhyloP100		-0.82

Splicing

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

Other links and lift over

dbSNP: rs9275618; hg19: chr6-32684387;