chr4-31441128-T-A

Variant names:

• chr4-31441128-T-A
• rs412253

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 0.701 in 152,054 control chromosomes in the GnomAD database, including 37,894 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 0.70 (37894 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.33
• Publications: 3 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 (SAS) allele frequency at 95% confidence interval = 0.767 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: 0.701 AC: 106515 AN: 151936 Hom.: 37875 Cov.: 33

Gnomad AFR AF: 0.600

Gnomad AMI AF: 0.868

Gnomad AMR AF: 0.613

Gnomad ASJ AF: 0.747

Gnomad EAS AF: 0.578

Gnomad SAS AF: 0.789

Gnomad FIN AF: 0.789

Gnomad MID AF: 0.691

Gnomad NFE AF: 0.767

Gnomad OTH AF: 0.702

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

GnomAD4 genome AF: 0.701 AC: 106575 AN: 152054 Hom.: 37894 Cov.: 33 AF XY: 0.701 AC XY: 52115 AN XY: 74314

African (AFR) AF: 0.600 AC: 24892 AN: 41474

American (AMR) AF: 0.613 AC: 9361 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.747 AC: 2593 AN: 3472

East Asian (EAS) AF: 0.578 AC: 2973 AN: 5146

South Asian (SAS) AF: 0.788 AC: 3804 AN: 4826

European-Finnish (FIN) AF: 0.789 AC: 8338 AN: 10566

Middle Eastern (MID) AF: 0.702 AC: 205 AN: 292

European-Non Finnish (NFE) AF: 0.767 AC: 52149 AN: 67980

Other (OTH) AF: 0.696 AC: 1470 AN: 2112

Alfa AF: 0.734 Hom.: 4781

Bravo AF: 0.677

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.15
DANN	Benign	0.39
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs412253; hg19: chr4-31442750;