6-32772894-G-C

Variant names:

• chr6-32772894-G-C
• rs2621421

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 0.683 in 148,306 control chromosomes in the GnomAD database, including 34,543 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 0.68 (34543 hom., cov: 24)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.884
• Publications: 17 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.787 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: 0.683 AC: 101203 AN: 148206 Hom.: 34536 Cov.: 24

Gnomad AFR AF: 0.674

Gnomad AMI AF: 0.773

Gnomad AMR AF: 0.673

Gnomad ASJ AF: 0.685

Gnomad EAS AF: 0.730

Gnomad SAS AF: 0.810

Gnomad FIN AF: 0.785

Gnomad MID AF: 0.804

Gnomad NFE AF: 0.660

Gnomad OTH AF: 0.700

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

GnomAD4 genome AF: 0.683 AC: 101248 AN: 148306 Hom.: 34543 Cov.: 24 AF XY: 0.690 AC XY: 49876 AN XY: 72246

African (AFR) AF: 0.674 AC: 27086 AN: 40196

American (AMR) AF: 0.673 AC: 9971 AN: 14816

Ashkenazi Jewish (ASJ) AF: 0.685 AC: 2357 AN: 3440

East Asian (EAS) AF: 0.731 AC: 3716 AN: 5086

South Asian (SAS) AF: 0.808 AC: 3799 AN: 4702

European-Finnish (FIN) AF: 0.785 AC: 7625 AN: 9712

Middle Eastern (MID) AF: 0.803 AC: 233 AN: 290

European-Non Finnish (NFE) AF: 0.660 AC: 44310 AN: 67094

Other (OTH) AF: 0.703 AC: 1452 AN: 2066

Alfa AF: 0.654 Hom.: 16154

Bravo AF: 0.665

Asia WGS AF: 0.778 AC: 2703 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.61
DANN	Benign	0.52
PhyloP100		-0.88

Splicing

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

Other links and lift over

dbSNP: rs2621421; hg19: chr6-32740671;