rs4719302

Variant names:

• chr7-12205994-G-A
• rs4719302

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 0.625 in 152,056 control chromosomes in the GnomAD database, including 30,569 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 0.62 (30569 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.175

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.788 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: 0.625 AC: 94913 AN: 151938 Hom.: 30534 Cov.: 32

Gnomad AFR AF: 0.795

Gnomad AMI AF: 0.443

Gnomad AMR AF: 0.623

Gnomad ASJ AF: 0.540

Gnomad EAS AF: 0.582

Gnomad SAS AF: 0.604

Gnomad FIN AF: 0.553

Gnomad MID AF: 0.604

Gnomad NFE AF: 0.545

Gnomad OTH AF: 0.594

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

GnomAD4 genome AF: 0.625 AC: 95007 AN: 152056 Hom.: 30569 Cov.: 32 AF XY: 0.627 AC XY: 46556 AN XY: 74302

Gnomad4 AFR AF: 0.796

Gnomad4 AMR AF: 0.623

Gnomad4 ASJ AF: 0.540

Gnomad4 EAS AF: 0.582

Gnomad4 SAS AF: 0.603

Gnomad4 FIN AF: 0.553

Gnomad4 NFE AF: 0.545

Gnomad4 OTH AF: 0.592

Alfa AF: 0.580 Hom.: 7997

Bravo AF: 0.635

Asia WGS AF: 0.605 AC: 2095 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.44
DANN	Benign	0.22

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4719302; hg19: chr7-12245620;