rs723147

Variant names:

• chr4-44544994-C-T
• rs723147

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;