4-156720838-T-G

Variant names:

• chr4-156720838-T-G
• rs1469244

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 0.465 in 152,060 control chromosomes in the GnomAD database, including 19,174 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 0.46 (19174 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0200

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.747 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: 0.465 AC: 70592 AN: 151942 Hom.: 19129 Cov.: 32

Gnomad AFR AF: 0.754

Gnomad AMI AF: 0.362

Gnomad AMR AF: 0.375

Gnomad ASJ AF: 0.424

Gnomad EAS AF: 0.332

Gnomad SAS AF: 0.608

Gnomad FIN AF: 0.275

Gnomad MID AF: 0.497

Gnomad NFE AF: 0.342

Gnomad OTH AF: 0.456

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

GnomAD4 genome AF: 0.465 AC: 70693 AN: 152060 Hom.: 19174 Cov.: 32 AF XY: 0.462 AC XY: 34353 AN XY: 74336

Gnomad4 AFR AF: 0.754

Gnomad4 AMR AF: 0.375

Gnomad4 ASJ AF: 0.424

Gnomad4 EAS AF: 0.332

Gnomad4 SAS AF: 0.608

Gnomad4 FIN AF: 0.275

Gnomad4 NFE AF: 0.342

Gnomad4 OTH AF: 0.456

Alfa AF: 0.334 Hom.: 1647

Bravo AF: 0.483

Asia WGS AF: 0.501 AC: 1738 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.80
DANN	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1469244; hg19: chr4-157641990;