rs255406

Variant names:

• chr5-63478387-A-G
• rs255406

Your query was ambiguous. Multiple possible variants found:

• chr5-63478387-A-G
• chr5-63478387-A-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 0.773 in 147,410 control chromosomes in the GnomAD database, including 44,088 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 0.77 (44088 hom., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.875
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.858 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: 0.773 AC: 113857 AN: 147302 Hom.: 44054 Cov.: 22

Gnomad AFR AF: 0.775

Gnomad AMI AF: 0.855

Gnomad AMR AF: 0.769

Gnomad ASJ AF: 0.723

Gnomad EAS AF: 0.880

Gnomad SAS AF: 0.761

Gnomad FIN AF: 0.788

Gnomad MID AF: 0.711

Gnomad NFE AF: 0.765

Gnomad OTH AF: 0.770

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

GnomAD4 genome AF: 0.773 AC: 113932 AN: 147410 Hom.: 44088 Cov.: 22 AF XY: 0.774 AC XY: 55389 AN XY: 71556

African (AFR) AF: 0.775 AC: 30916 AN: 39890

American (AMR) AF: 0.769 AC: 11178 AN: 14538

Ashkenazi Jewish (ASJ) AF: 0.723 AC: 2497 AN: 3456

East Asian (EAS) AF: 0.880 AC: 4378 AN: 4976

South Asian (SAS) AF: 0.761 AC: 3534 AN: 4642

European-Finnish (FIN) AF: 0.788 AC: 7307 AN: 9274

Middle Eastern (MID) AF: 0.698 AC: 201 AN: 288

European-Non Finnish (NFE) AF: 0.765 AC: 51573 AN: 67402

Other (OTH) AF: 0.772 AC: 1580 AN: 2046

Alfa AF: 0.768 Hom.: 7419

Bravo AF: 0.775

Asia WGS AF: 0.811 AC: 2818 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.6
DANN	Benign	0.44
PhyloP100		-0.88

Splicing

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

Other links and lift over

dbSNP: rs255406; hg19: chr5-62774214; COSMIC: COSV51187594;