rs1494066

Variant names:

• chr5-2970206-A-G
• rs1494066

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 0.72 in 152,184 control chromosomes in the GnomAD database, including 39,978 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 0.72 (39978 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.20
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.777 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: 0.720 AC: 109502 AN: 152066 Hom.: 39960 Cov.: 34

Gnomad AFR AF: 0.587

Gnomad AMI AF: 0.590

Gnomad AMR AF: 0.773

Gnomad ASJ AF: 0.685

Gnomad EAS AF: 0.797

Gnomad SAS AF: 0.756

Gnomad FIN AF: 0.802

Gnomad MID AF: 0.696

Gnomad NFE AF: 0.772

Gnomad OTH AF: 0.734

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

GnomAD4 genome AF: 0.720 AC: 109577 AN: 152184 Hom.: 39978 Cov.: 34 AF XY: 0.724 AC XY: 53859 AN XY: 74384

African (AFR) AF: 0.587 AC: 24352 AN: 41502

American (AMR) AF: 0.772 AC: 11818 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.685 AC: 2379 AN: 3472

East Asian (EAS) AF: 0.797 AC: 4130 AN: 5180

South Asian (SAS) AF: 0.757 AC: 3642 AN: 4814

European-Finnish (FIN) AF: 0.802 AC: 8502 AN: 10602

Middle Eastern (MID) AF: 0.690 AC: 203 AN: 294

European-Non Finnish (NFE) AF: 0.772 AC: 52466 AN: 67998

Other (OTH) AF: 0.733 AC: 1549 AN: 2114

Alfa AF: 0.754 Hom.: 70151

Bravo AF: 0.711

Asia WGS AF: 0.761 AC: 2647 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.019
DANN	Benign	0.27
PhyloP100		-4.2

Splicing

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

Other links and lift over

dbSNP: rs1494066; hg19: chr5-2970320;