4-31441128-T-A

Variant names:

• chr4-31441128-T-A
• rs412253

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.600

Gnomad4 AMR AF: 0.613

Gnomad4 ASJ AF: 0.747

Gnomad4 EAS AF: 0.578

Gnomad4 SAS AF: 0.788

Gnomad4 FIN AF: 0.789

Gnomad4 NFE AF: 0.767

Gnomad4 OTH AF: 0.696

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs412253; hg19: chr4-31442750;