rs4234898

Variant names:

• chr4-156077389-T-C
• rs4234898

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 0.849 in 152,048 control chromosomes in the GnomAD database, including 54,980 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 0.85 (54980 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.28
• Publications: 24 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.877 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: 0.849 AC: 129014 AN: 151930 Hom.: 54927 Cov.: 31

Gnomad AFR AF: 0.785

Gnomad AMI AF: 0.967

Gnomad AMR AF: 0.872

Gnomad ASJ AF: 0.853

Gnomad EAS AF: 0.872

Gnomad SAS AF: 0.827

Gnomad FIN AF: 0.836

Gnomad MID AF: 0.816

Gnomad NFE AF: 0.882

Gnomad OTH AF: 0.866

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

GnomAD4 genome AF: 0.849 AC: 129124 AN: 152048 Hom.: 54980 Cov.: 31 AF XY: 0.848 AC XY: 63003 AN XY: 74296

African (AFR) AF: 0.786 AC: 32574 AN: 41462

American (AMR) AF: 0.873 AC: 13332 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.853 AC: 2961 AN: 3472

East Asian (EAS) AF: 0.873 AC: 4504 AN: 5162

South Asian (SAS) AF: 0.828 AC: 3984 AN: 4814

European-Finnish (FIN) AF: 0.836 AC: 8814 AN: 10544

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

European-Non Finnish (NFE) AF: 0.882 AC: 60004 AN: 67998

Other (OTH) AF: 0.865 AC: 1826 AN: 2110

Alfa AF: 0.871 Hom.: 195071

Bravo AF: 0.850

Asia WGS AF: 0.840 AC: 2923 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.14
DANN	Benign	0.65
PhyloP100		-4.3

Splicing

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

Other links and lift over

dbSNP: rs4234898; hg19: chr4-156998541;