7-100717894-A-G

Variant names:

• chr7-100717894-A-G
• rs1734907

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;