rs4703129

Variant names:

• chr5-98553032-C-A
• rs4703129

Your query was ambiguous. Multiple possible variants found:

• chr5-98553032-C-A
• chr5-98553032-C-G
• chr5-98553032-C-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 0.34 in 151,828 control chromosomes in the GnomAD database, including 11,016 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 0.34 (11016 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.380
• Publications: 11 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.618 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: 0.340 AC: 51605 AN: 151710 Hom.: 11010 Cov.: 31

Gnomad AFR AF: 0.0794

Gnomad AMI AF: 0.371

Gnomad AMR AF: 0.451

Gnomad ASJ AF: 0.432

Gnomad EAS AF: 0.636

Gnomad SAS AF: 0.349

Gnomad FIN AF: 0.586

Gnomad MID AF: 0.443

Gnomad NFE AF: 0.406

Gnomad OTH AF: 0.372

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

GnomAD4 genome AF: 0.340 AC: 51616 AN: 151828 Hom.: 11016 Cov.: 31 AF XY: 0.352 AC XY: 26145 AN XY: 74192

African (AFR) AF: 0.0791 AC: 3282 AN: 41474

American (AMR) AF: 0.451 AC: 6878 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.432 AC: 1497 AN: 3466

East Asian (EAS) AF: 0.636 AC: 3278 AN: 5156

South Asian (SAS) AF: 0.351 AC: 1690 AN: 4818

European-Finnish (FIN) AF: 0.586 AC: 6150 AN: 10488

Middle Eastern (MID) AF: 0.446 AC: 131 AN: 294

European-Non Finnish (NFE) AF: 0.406 AC: 27588 AN: 67888

Other (OTH) AF: 0.374 AC: 784 AN: 2094

Alfa AF: 0.376 Hom.: 19955

Bravo AF: 0.322

Asia WGS AF: 0.415 AC: 1423 AN: 3426

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	3.3
DANN	Benign	0.58
PhyloP100		-0.38

Splicing

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

Other links and lift over

dbSNP: rs4703129; hg19: chr5-97888736;