rs963903

Variant names:

• chr4-137886021-A-G
• rs963903

Your query was ambiguous. Multiple possible variants found:

• chr4-137886021-A-G
• chr4-137886021-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 0.355 in 151,892 control chromosomes in the GnomAD database, including 10,072 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 0.36 (10072 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.50
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.403 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: 0.355 AC: 53917 AN: 151774 Hom.: 10053 Cov.: 33

Gnomad AFR AF: 0.300

Gnomad AMI AF: 0.595

Gnomad AMR AF: 0.343

Gnomad ASJ AF: 0.516

Gnomad EAS AF: 0.0919

Gnomad SAS AF: 0.271

Gnomad FIN AF: 0.345

Gnomad MID AF: 0.449

Gnomad NFE AF: 0.407

Gnomad OTH AF: 0.377

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

GnomAD4 genome AF: 0.355 AC: 53976 AN: 151892 Hom.: 10072 Cov.: 33 AF XY: 0.350 AC XY: 26005 AN XY: 74296

African (AFR) AF: 0.300 AC: 12451 AN: 41504

American (AMR) AF: 0.345 AC: 5264 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.516 AC: 1791 AN: 3470

East Asian (EAS) AF: 0.0921 AC: 477 AN: 5180

South Asian (SAS) AF: 0.270 AC: 1297 AN: 4812

European-Finnish (FIN) AF: 0.345 AC: 3606 AN: 10448

Middle Eastern (MID) AF: 0.466 AC: 135 AN: 290

European-Non Finnish (NFE) AF: 0.407 AC: 27612 AN: 67894

Other (OTH) AF: 0.381 AC: 802 AN: 2104

Alfa AF: 0.375 Hom.: 1399

Bravo AF: 0.356

Asia WGS AF: 0.221 AC: 765 AN: 3446

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	5.2
DANN	Benign	0.74
PhyloP100		1.5

Splicing

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

Other links and lift over

dbSNP: rs963903; hg19: chr4-138807175;