rs4727443

chr7-99995723-C-Achr7-99995723-C-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 0.346 in 151,912 control chromosomes in the GnomAD database, including 10,474 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 0.35 (10474 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.634

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.625 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.346 AC: 52535 AN: 151794 Hom.: 10470 Cov.: 31

Gnomad AFR AF: 0.160

Gnomad AMI AF: 0.505

Gnomad AMR AF: 0.473

Gnomad ASJ AF: 0.440

Gnomad EAS AF: 0.644

Gnomad SAS AF: 0.422

Gnomad FIN AF: 0.345

Gnomad MID AF: 0.500

Gnomad NFE AF: 0.394

Gnomad OTH AF: 0.387

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

GnomAD4 genome AF: 0.346 AC: 52555 AN: 151912 Hom.: 10474 Cov.: 31 AF XY: 0.352 AC XY: 26110 AN XY: 74276

Gnomad4 AFR AF: 0.160

Gnomad4 AMR AF: 0.473

Gnomad4 ASJ AF: 0.440

Gnomad4 EAS AF: 0.644

Gnomad4 SAS AF: 0.423

Gnomad4 FIN AF: 0.345

Gnomad4 NFE AF: 0.394

Gnomad4 OTH AF: 0.391

Alfa AF: 0.390 Hom.: 23792

Bravo AF: 0.350

Asia WGS AF: 0.490 AC: 1702 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
Cadd	Benign	1.1
Dann	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4727443; hg19: chr7-99593346;