rs2747479

Variant names:

• chr6-33378409-C-A
• rs2747479

Your query was ambiguous. Multiple possible variants found:

• chr6-33378409-C-A
• chr6-33378409-C-G
• chr6-33378409-C-T

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 0.442 in 151,656 control chromosomes in the GnomAD database, including 15,760 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 0.44 (15760 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.598
• Publications: 12 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.596 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: 0.442 AC: 67001 AN: 151540 Hom.: 15733 Cov.: 32

Gnomad AFR AF: 0.590

Gnomad AMI AF: 0.379

Gnomad AMR AF: 0.421

Gnomad ASJ AF: 0.423

Gnomad EAS AF: 0.613

Gnomad SAS AF: 0.511

Gnomad FIN AF: 0.270

Gnomad MID AF: 0.446

Gnomad NFE AF: 0.366

Gnomad OTH AF: 0.465

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

GnomAD4 genome AF: 0.442 AC: 67078 AN: 151656 Hom.: 15760 Cov.: 32 AF XY: 0.440 AC XY: 32632 AN XY: 74108

African (AFR) AF: 0.590 AC: 24411 AN: 41342

American (AMR) AF: 0.421 AC: 6402 AN: 15216

Ashkenazi Jewish (ASJ) AF: 0.423 AC: 1469 AN: 3470

East Asian (EAS) AF: 0.614 AC: 3169 AN: 5164

South Asian (SAS) AF: 0.511 AC: 2462 AN: 4818

European-Finnish (FIN) AF: 0.270 AC: 2818 AN: 10428

Middle Eastern (MID) AF: 0.456 AC: 134 AN: 294

European-Non Finnish (NFE) AF: 0.366 AC: 24887 AN: 67914

Other (OTH) AF: 0.467 AC: 982 AN: 2102

Alfa AF: 0.394 Hom.: 12273

Bravo AF: 0.457

Asia WGS AF: 0.591 AC: 2056 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.31
DANN	Benign	0.66
PhyloP100		-0.60

Splicing

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

Other links and lift over

dbSNP: rs2747479; hg19: chr6-33346186;