rs217386

chr7-44561096-G-A

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 0.405 in 151,984 control chromosomes in the GnomAD database, including 13,153 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 0.40 (13153 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.03

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.465 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: 0.405 AC: 61529 AN: 151866 Hom.: 13154 Cov.: 32

Gnomad AFR AF: 0.471

Gnomad AMI AF: 0.444

Gnomad AMR AF: 0.339

Gnomad ASJ AF: 0.497

Gnomad EAS AF: 0.0270

Gnomad SAS AF: 0.283

Gnomad FIN AF: 0.300

Gnomad MID AF: 0.516

Gnomad NFE AF: 0.427

Gnomad OTH AF: 0.438

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

GnomAD4 genome AF: 0.405 AC: 61553 AN: 151984 Hom.: 13153 Cov.: 32 AF XY: 0.392 AC XY: 29140 AN XY: 74292

Gnomad4 AFR AF: 0.471

Gnomad4 AMR AF: 0.339

Gnomad4 ASJ AF: 0.497

Gnomad4 EAS AF: 0.0272

Gnomad4 SAS AF: 0.282

Gnomad4 FIN AF: 0.300

Gnomad4 NFE AF: 0.427

Gnomad4 OTH AF: 0.434

Alfa AF: 0.413 Hom.: 5226

Bravo AF: 0.412

Asia WGS AF: 0.184 AC: 641 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	0.39
Dann	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs217386; hg19: chr7-44600695;