4-105127203-T-G

Variant names:

• chr4-105127203-T-G
• rs1541374

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 0.744 in 152,034 control chromosomes in the GnomAD database, including 42,381 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 0.74 (42381 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.289

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.825 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: 0.744 AC: 112955 AN: 151916 Hom.: 42323 Cov.: 33

Gnomad AFR AF: 0.832

Gnomad AMI AF: 0.655

Gnomad AMR AF: 0.765

Gnomad ASJ AF: 0.767

Gnomad EAS AF: 0.818

Gnomad SAS AF: 0.731

Gnomad FIN AF: 0.733

Gnomad MID AF: 0.787

Gnomad NFE AF: 0.681

Gnomad OTH AF: 0.756

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

GnomAD4 genome AF: 0.744 AC: 113075 AN: 152034 Hom.: 42381 Cov.: 33 AF XY: 0.750 AC XY: 55699 AN XY: 74312

Gnomad4 AFR AF: 0.832

Gnomad4 AMR AF: 0.765

Gnomad4 ASJ AF: 0.767

Gnomad4 EAS AF: 0.818

Gnomad4 SAS AF: 0.731

Gnomad4 FIN AF: 0.733

Gnomad4 NFE AF: 0.681

Gnomad4 OTH AF: 0.759

Alfa AF: 0.691 Hom.: 56119

Bravo AF: 0.759

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	3.0
DANN	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1541374; hg19: chr4-106048360;