6-32772894-G-C

Variant names:

• chr6-32772894-G-C
• rs2621421

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.674

Gnomad4 AMR AF: 0.673

Gnomad4 ASJ AF: 0.685

Gnomad4 EAS AF: 0.731

Gnomad4 SAS AF: 0.808

Gnomad4 FIN AF: 0.785

Gnomad4 NFE AF: 0.660

Gnomad4 OTH AF: 0.703

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2621421; hg19: chr6-32740671;