rs1970883

Variant names:

• chr4-17360490-A-G
• rs1970883

Your query was ambiguous. Multiple possible variants found:

• chr4-17360490-A-G
• chr4-17360490-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 0.878 in 152,076 control chromosomes in the GnomAD database, including 59,423 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 0.88 (59423 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.77
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.954 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: 0.878 AC: 133357 AN: 151958 Hom.: 59365 Cov.: 30

Gnomad AFR AF: 0.730

Gnomad AMI AF: 0.947

Gnomad AMR AF: 0.913

Gnomad ASJ AF: 0.965

Gnomad EAS AF: 0.742

Gnomad SAS AF: 0.939

Gnomad FIN AF: 0.873

Gnomad MID AF: 0.965

Gnomad NFE AF: 0.960

Gnomad OTH AF: 0.893

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

GnomAD4 genome AF: 0.878 AC: 133475 AN: 152076 Hom.: 59423 Cov.: 30 AF XY: 0.876 AC XY: 65110 AN XY: 74338

African (AFR) AF: 0.730 AC: 30244 AN: 41424

American (AMR) AF: 0.913 AC: 13952 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.965 AC: 3347 AN: 3468

East Asian (EAS) AF: 0.743 AC: 3821 AN: 5144

South Asian (SAS) AF: 0.940 AC: 4534 AN: 4824

European-Finnish (FIN) AF: 0.873 AC: 9239 AN: 10582

Middle Eastern (MID) AF: 0.963 AC: 283 AN: 294

European-Non Finnish (NFE) AF: 0.960 AC: 65300 AN: 68026

Other (OTH) AF: 0.895 AC: 1891 AN: 2114

Alfa AF: 0.886 Hom.: 11191

Bravo AF: 0.870

Asia WGS AF: 0.860 AC: 2991 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.23
DANN	Benign	0.31
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs1970883; hg19: chr4-17362113;