chr4-17437723-A-G

Position:

• chr4-17437723-A-G

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 0.427 in 152,014 control chromosomes in the GnomAD database, including 14,387 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 0.43 (14387 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.123

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.477 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.427 AC: 64834 AN: 151896 Hom.: 14385 Cov.: 32

Gnomad AFR AF: 0.420

Gnomad AMI AF: 0.510

Gnomad AMR AF: 0.335

Gnomad ASJ AF: 0.369

Gnomad EAS AF: 0.105

Gnomad SAS AF: 0.342

Gnomad FIN AF: 0.443

Gnomad MID AF: 0.379

Gnomad NFE AF: 0.481

Gnomad OTH AF: 0.433

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

GnomAD4 genome AF: 0.427 AC: 64860 AN: 152014 Hom.: 14387 Cov.: 32 AF XY: 0.421 AC XY: 31262 AN XY: 74312

Gnomad4 AFR AF: 0.420

Gnomad4 AMR AF: 0.335

Gnomad4 ASJ AF: 0.369

Gnomad4 EAS AF: 0.104

Gnomad4 SAS AF: 0.342

Gnomad4 FIN AF: 0.443

Gnomad4 NFE AF: 0.481

Gnomad4 OTH AF: 0.431

Alfa AF: 0.462 Hom.: 27245

Bravo AF: 0.419

Asia WGS AF: 0.256 AC: 891 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	6.4
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7671329; hg19: chr4-17439346;