rs1948983

Variant names:

• chr4-115323641-G-C
• rs1948983

Your query was ambiguous. Multiple possible variants found:

• chr4-115323641-G-C
• chr4-115323641-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 0.556 in 151,908 control chromosomes in the GnomAD database, including 24,201 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 0.56 (24201 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.216
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.61).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.649 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.556 AC: 84471 AN: 151790 Hom.: 24204 Cov.: 32

Gnomad AFR AF: 0.434

Gnomad AMI AF: 0.555

Gnomad AMR AF: 0.506

Gnomad ASJ AF: 0.529

Gnomad EAS AF: 0.669

Gnomad SAS AF: 0.487

Gnomad FIN AF: 0.693

Gnomad MID AF: 0.547

Gnomad NFE AF: 0.619

Gnomad OTH AF: 0.552

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

GnomAD4 genome AF: 0.556 AC: 84494 AN: 151908 Hom.: 24201 Cov.: 32 AF XY: 0.557 AC XY: 41338 AN XY: 74254

African (AFR) AF: 0.434 AC: 17979 AN: 41422

American (AMR) AF: 0.506 AC: 7712 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.529 AC: 1834 AN: 3468

East Asian (EAS) AF: 0.668 AC: 3423 AN: 5128

South Asian (SAS) AF: 0.487 AC: 2345 AN: 4814

European-Finnish (FIN) AF: 0.693 AC: 7323 AN: 10560

Middle Eastern (MID) AF: 0.544 AC: 160 AN: 294

European-Non Finnish (NFE) AF: 0.619 AC: 42049 AN: 67952

Other (OTH) AF: 0.551 AC: 1163 AN: 2110

Alfa AF: 0.573 Hom.: 3122

Bravo AF: 0.542

Asia WGS AF: 0.534 AC: 1855 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.61
CADD	Benign	1.7
DANN	Benign	0.52
PhyloP100		-0.22

Splicing

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

Other links and lift over

dbSNP: rs1948983; hg19: chr4-116244797;