chr4-4251229-A-G

Variant names:

• chr4-4251229-A-G
• rs2980098

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 0.418 in 151,870 control chromosomes in the GnomAD database, including 14,129 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 0.42 (14129 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.368
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.551 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: 0.418 AC: 63472 AN: 151752 Hom.: 14100 Cov.: 31

Gnomad AFR AF: 0.557

Gnomad AMI AF: 0.333

Gnomad AMR AF: 0.478

Gnomad ASJ AF: 0.309

Gnomad EAS AF: 0.401

Gnomad SAS AF: 0.441

Gnomad FIN AF: 0.270

Gnomad MID AF: 0.285

Gnomad NFE AF: 0.352

Gnomad OTH AF: 0.393

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

GnomAD4 genome AF: 0.418 AC: 63552 AN: 151870 Hom.: 14129 Cov.: 31 AF XY: 0.416 AC XY: 30869 AN XY: 74222

African (AFR) AF: 0.557 AC: 23035 AN: 41374

American (AMR) AF: 0.478 AC: 7290 AN: 15238

Ashkenazi Jewish (ASJ) AF: 0.309 AC: 1073 AN: 3470

East Asian (EAS) AF: 0.401 AC: 2073 AN: 5172

South Asian (SAS) AF: 0.442 AC: 2124 AN: 4808

European-Finnish (FIN) AF: 0.270 AC: 2849 AN: 10548

Middle Eastern (MID) AF: 0.296 AC: 87 AN: 294

European-Non Finnish (NFE) AF: 0.351 AC: 23882 AN: 67948

Other (OTH) AF: 0.396 AC: 835 AN: 2106

Alfa AF: 0.378 Hom.: 34879

Bravo AF: 0.440

Asia WGS AF: 0.446 AC: 1548 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	2.4
DANN	Benign	0.29
PhyloP100		-0.37

Splicing

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

Other links and lift over

dbSNP: rs2980098; hg19: chr4-4252956;