6-2651753-A-G

Variant names:

• chr6-2651753-A-G
• rs9328112

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 0.532 in 152,068 control chromosomes in the GnomAD database, including 22,354 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 0.53 (22354 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.917

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.635 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: 0.532 AC: 80819 AN: 151948 Hom.: 22334 Cov.: 32

Gnomad AFR AF: 0.366

Gnomad AMI AF: 0.437

Gnomad AMR AF: 0.568

Gnomad ASJ AF: 0.587

Gnomad EAS AF: 0.577

Gnomad SAS AF: 0.653

Gnomad FIN AF: 0.596

Gnomad MID AF: 0.601

Gnomad NFE AF: 0.600

Gnomad OTH AF: 0.551

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

GnomAD4 genome AF: 0.532 AC: 80878 AN: 152068 Hom.: 22354 Cov.: 32 AF XY: 0.538 AC XY: 40034 AN XY: 74344

Gnomad4 AFR AF: 0.366

Gnomad4 AMR AF: 0.568

Gnomad4 ASJ AF: 0.587

Gnomad4 EAS AF: 0.576

Gnomad4 SAS AF: 0.654

Gnomad4 FIN AF: 0.596

Gnomad4 NFE AF: 0.600

Gnomad4 OTH AF: 0.554

Alfa AF: 0.564 Hom.: 13343

Bravo AF: 0.518

Asia WGS AF: 0.590 AC: 2055 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.25
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9328112; hg19: chr6-2651987;