rs1990702

Variant names:

• chr2-169120005-T-C
• rs1990702

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 0.758 in 152,150 control chromosomes in the GnomAD database, including 44,118 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 0.76 (44118 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.124
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.796 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: 0.758 AC: 115271 AN: 152030 Hom.: 44078 Cov.: 32

Gnomad AFR AF: 0.804

Gnomad AMI AF: 0.751

Gnomad AMR AF: 0.781

Gnomad ASJ AF: 0.681

Gnomad EAS AF: 0.416

Gnomad SAS AF: 0.774

Gnomad FIN AF: 0.747

Gnomad MID AF: 0.829

Gnomad NFE AF: 0.755

Gnomad OTH AF: 0.766

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

GnomAD4 genome AF: 0.758 AC: 115364 AN: 152150 Hom.: 44118 Cov.: 32 AF XY: 0.757 AC XY: 56289 AN XY: 74358

African (AFR) AF: 0.804 AC: 33365 AN: 41514

American (AMR) AF: 0.781 AC: 11952 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.681 AC: 2364 AN: 3470

East Asian (EAS) AF: 0.416 AC: 2147 AN: 5156

South Asian (SAS) AF: 0.773 AC: 3717 AN: 4808

European-Finnish (FIN) AF: 0.747 AC: 7906 AN: 10588

Middle Eastern (MID) AF: 0.827 AC: 243 AN: 294

European-Non Finnish (NFE) AF: 0.755 AC: 51364 AN: 67996

Other (OTH) AF: 0.768 AC: 1621 AN: 2112

Alfa AF: 0.760 Hom.: 11718

Bravo AF: 0.759

Asia WGS AF: 0.650 AC: 2261 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	4.7
DANN	Benign	0.45
PhyloP100		-0.12

Splicing

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

Other links and lift over

dbSNP: rs1990702; hg19: chr2-169976515;