rs499697

Variant names:

• chr1-152520678-G-A
• rs499697

Your query was ambiguous. Multiple possible variants found:

• chr1-152520678-G-A
• chr1-152520678-G-C
• chr1-152520678-G-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 0.792 in 152,170 control chromosomes in the GnomAD database, including 48,190 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 0.79 (48190 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00700
• Publications: 32 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.922 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: 0.791 AC: 120345 AN: 152052 Hom.: 48127 Cov.: 31

Gnomad AFR AF: 0.930

Gnomad AMI AF: 0.724

Gnomad AMR AF: 0.788

Gnomad ASJ AF: 0.805

Gnomad EAS AF: 0.774

Gnomad SAS AF: 0.729

Gnomad FIN AF: 0.783

Gnomad MID AF: 0.839

Gnomad NFE AF: 0.715

Gnomad OTH AF: 0.786

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

GnomAD4 genome AF: 0.792 AC: 120466 AN: 152170 Hom.: 48190 Cov.: 31 AF XY: 0.794 AC XY: 59043 AN XY: 74402

African (AFR) AF: 0.930 AC: 38644 AN: 41546

American (AMR) AF: 0.788 AC: 12043 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.805 AC: 2791 AN: 3468

East Asian (EAS) AF: 0.773 AC: 4000 AN: 5174

South Asian (SAS) AF: 0.728 AC: 3512 AN: 4822

European-Finnish (FIN) AF: 0.783 AC: 8283 AN: 10584

Middle Eastern (MID) AF: 0.847 AC: 249 AN: 294

European-Non Finnish (NFE) AF: 0.715 AC: 48618 AN: 67972

Other (OTH) AF: 0.789 AC: 1666 AN: 2112

Alfa AF: 0.740 Hom.: 139278

Bravo AF: 0.799

Asia WGS AF: 0.777 AC: 2703 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	3.6
DANN	Benign	0.61
PhyloP100		-0.0070

Splicing

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

Other links and lift over

dbSNP: rs499697; hg19: chr1-152493154;