4-156720838-T-G

Variant names:

• chr4-156720838-T-G
• rs1469244

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 0.465 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
• Publications: 7 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.754 AC: 31279 AN: 41478

American (AMR) AF: 0.375 AC: 5729 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.424 AC: 1470 AN: 3468

East Asian (EAS) AF: 0.332 AC: 1719 AN: 5176

South Asian (SAS) AF: 0.608 AC: 2932 AN: 4822

European-Finnish (FIN) AF: 0.275 AC: 2907 AN: 10578

Middle Eastern (MID) AF: 0.497 AC: 145 AN: 292

European-Non Finnish (NFE) AF: 0.342 AC: 23222 AN: 67958

Other (OTH) AF: 0.456 AC: 961 AN: 2106

Alfa AF: 0.349 Hom.: 1865

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
PhyloP100		0.020

Splicing

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

Other links and lift over

dbSNP: rs1469244; hg19: chr4-157641990;