6-46743287-C-G

Variant names:

• chr6-46743287-C-G
• rs12211537

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 0.347 in 152,028 control chromosomes in the GnomAD database, including 11,665 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 0.35 (11665 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.194
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.618 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: 0.347 AC: 52766 AN: 151908 Hom.: 11663 Cov.: 32

Gnomad AFR AF: 0.0862

Gnomad AMI AF: 0.346

Gnomad AMR AF: 0.353

Gnomad ASJ AF: 0.298

Gnomad EAS AF: 0.636

Gnomad SAS AF: 0.229

Gnomad FIN AF: 0.539

Gnomad MID AF: 0.218

Gnomad NFE AF: 0.465

Gnomad OTH AF: 0.334

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

GnomAD4 genome AF: 0.347 AC: 52771 AN: 152028 Hom.: 11665 Cov.: 32 AF XY: 0.351 AC XY: 26047 AN XY: 74298

African (AFR) AF: 0.0859 AC: 3567 AN: 41508

American (AMR) AF: 0.353 AC: 5400 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.298 AC: 1033 AN: 3470

East Asian (EAS) AF: 0.636 AC: 3282 AN: 5162

South Asian (SAS) AF: 0.230 AC: 1110 AN: 4816

European-Finnish (FIN) AF: 0.539 AC: 5682 AN: 10544

Middle Eastern (MID) AF: 0.228 AC: 67 AN: 294

European-Non Finnish (NFE) AF: 0.465 AC: 31610 AN: 67932

Other (OTH) AF: 0.334 AC: 706 AN: 2116

Alfa AF: 0.417 Hom.: 2047

Bravo AF: 0.325

Asia WGS AF: 0.379 AC: 1316 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.1
DANN	Benign	0.56
PhyloP100		-0.19

Splicing

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

Other links and lift over

dbSNP: rs12211537; hg19: chr6-46711024;