rs646984

Variant names:

• chr6-32608815-A-C
• rs646984

Your query was ambiguous. Multiple possible variants found:

• chr6-32608815-A-C
• chr6-32608815-A-G

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 0.376 in 151,262 control chromosomes in the GnomAD database, including 11,005 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 0.38 (11005 hom., cov: 27)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.552
• Publications: 18 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.459 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: 0.376 AC: 56841 AN: 151144 Hom.: 11001 Cov.: 27

Gnomad AFR AF: 0.306

Gnomad AMI AF: 0.446

Gnomad AMR AF: 0.468

Gnomad ASJ AF: 0.420

Gnomad EAS AF: 0.314

Gnomad SAS AF: 0.365

Gnomad FIN AF: 0.396

Gnomad MID AF: 0.364

Gnomad NFE AF: 0.398

Gnomad OTH AF: 0.383

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

GnomAD4 genome AF: 0.376 AC: 56872 AN: 151262 Hom.: 11005 Cov.: 27 AF XY: 0.377 AC XY: 27851 AN XY: 73898

African (AFR) AF: 0.306 AC: 12599 AN: 41224

American (AMR) AF: 0.468 AC: 7118 AN: 15202

Ashkenazi Jewish (ASJ) AF: 0.420 AC: 1451 AN: 3456

East Asian (EAS) AF: 0.315 AC: 1603 AN: 5094

South Asian (SAS) AF: 0.363 AC: 1733 AN: 4778

European-Finnish (FIN) AF: 0.396 AC: 4154 AN: 10498

Middle Eastern (MID) AF: 0.343 AC: 98 AN: 286

European-Non Finnish (NFE) AF: 0.398 AC: 26922 AN: 67726

Other (OTH) AF: 0.378 AC: 792 AN: 2096

Alfa AF: 0.358 Hom.: 2760

Bravo AF: 0.385

Asia WGS AF: 0.335 AC: 1165 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.9
DANN	Benign	0.32
PhyloP100		-0.55

Splicing

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

Other links and lift over

dbSNP: rs646984; hg19: chr6-32576592;