rs723147

Positions:

• chr4-44544994-C-T

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 0.142 in 152,100 control chromosomes in the GnomAD database, including 2,038 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 0.14 (2038 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.109

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.269 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: 0.142 AC: 21531 AN: 151982 Hom.: 2038 Cov.: 32

Gnomad AFR AF: 0.273

Gnomad AMI AF: 0.107

Gnomad AMR AF: 0.0834

Gnomad ASJ AF: 0.103

Gnomad EAS AF: 0.103

Gnomad SAS AF: 0.0704

Gnomad FIN AF: 0.0796

Gnomad MID AF: 0.0538

Gnomad NFE AF: 0.0958

Gnomad OTH AF: 0.121

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

GnomAD4 genome AF: 0.142 AC: 21538 AN: 152100 Hom.: 2038 Cov.: 32 AF XY: 0.137 AC XY: 10173 AN XY: 74360

Gnomad4 AFR AF: 0.273

Gnomad4 AMR AF: 0.0832

Gnomad4 ASJ AF: 0.103

Gnomad4 EAS AF: 0.103

Gnomad4 SAS AF: 0.0692

Gnomad4 FIN AF: 0.0796

Gnomad4 NFE AF: 0.0958

Gnomad4 OTH AF: 0.121

Alfa AF: 0.126 Hom.: 204

Bravo AF: 0.147

Asia WGS AF: 0.111 AC: 388 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.1
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs723147; hg19: chr4-44547011;