6-32608701-T-C

Variant names:

• chr6-32608701-T-C
• rs9271100

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 0.745 in 150,784 control chromosomes in the GnomAD database, including 42,077 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 0.74 (42077 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.261
• Publications: 81 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.783 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: 0.745 AC: 112188 AN: 150662 Hom.: 42042 Cov.: 29

Gnomad AFR AF: 0.767

Gnomad AMI AF: 0.689

Gnomad AMR AF: 0.788

Gnomad ASJ AF: 0.787

Gnomad EAS AF: 0.803

Gnomad SAS AF: 0.728

Gnomad FIN AF: 0.656

Gnomad MID AF: 0.860

Gnomad NFE AF: 0.729

Gnomad OTH AF: 0.775

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

GnomAD4 genome AF: 0.745 AC: 112276 AN: 150784 Hom.: 42077 Cov.: 29 AF XY: 0.742 AC XY: 54666 AN XY: 73696

African (AFR) AF: 0.767 AC: 31408 AN: 40940

American (AMR) AF: 0.788 AC: 11980 AN: 15208

Ashkenazi Jewish (ASJ) AF: 0.787 AC: 2720 AN: 3456

East Asian (EAS) AF: 0.804 AC: 4083 AN: 5078

South Asian (SAS) AF: 0.727 AC: 3468 AN: 4768

European-Finnish (FIN) AF: 0.656 AC: 6844 AN: 10440

Middle Eastern (MID) AF: 0.849 AC: 248 AN: 292

European-Non Finnish (NFE) AF: 0.729 AC: 49295 AN: 67614

Other (OTH) AF: 0.771 AC: 1607 AN: 2084

Alfa AF: 0.743 Hom.: 131597

Bravo AF: 0.759

Asia WGS AF: 0.710 AC: 2471 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	10
DANN	Benign	0.78
PhyloP100		0.26

Splicing

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

Other links and lift over

dbSNP: rs9271100; hg19: chr6-32576478;