rs1734907

chr7-100717894-A-Gchr7-100717894-A-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 0.844 in 152,180 control chromosomes in the GnomAD database, including 54,298 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 0.84 (54298 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.633

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.913 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: 0.844 AC: 128353 AN: 152062 Hom.: 54259 Cov.: 32

Gnomad AFR AF: 0.833

Gnomad AMI AF: 0.759

Gnomad AMR AF: 0.893

Gnomad ASJ AF: 0.908

Gnomad EAS AF: 0.935

Gnomad SAS AF: 0.779

Gnomad FIN AF: 0.793

Gnomad MID AF: 0.877

Gnomad NFE AF: 0.843

Gnomad OTH AF: 0.858

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

GnomAD4 genome AF: 0.844 AC: 128449 AN: 152180 Hom.: 54298 Cov.: 32 AF XY: 0.843 AC XY: 62719 AN XY: 74382

Gnomad4 AFR AF: 0.833

Gnomad4 AMR AF: 0.893

Gnomad4 ASJ AF: 0.908

Gnomad4 EAS AF: 0.935

Gnomad4 SAS AF: 0.780

Gnomad4 FIN AF: 0.793

Gnomad4 NFE AF: 0.843

Gnomad4 OTH AF: 0.859

Alfa AF: 0.850 Hom.: 93552

Bravo AF: 0.853

Asia WGS AF: 0.852 AC: 2965 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.79
Dann	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1734907; hg19: chr7-100315517;