rs41750

chr7-116808946-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 0.631 in 152,022 control chromosomes in the GnomAD database, including 30,741 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 0.63 (30741 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.821

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.88 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: 0.631 AC: 95807 AN: 151904 Hom.: 30734 Cov.: 32

Gnomad AFR AF: 0.552

Gnomad AMI AF: 0.712

Gnomad AMR AF: 0.642

Gnomad ASJ AF: 0.719

Gnomad EAS AF: 0.900

Gnomad SAS AF: 0.816

Gnomad FIN AF: 0.671

Gnomad MID AF: 0.649

Gnomad NFE AF: 0.631

Gnomad OTH AF: 0.626

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

GnomAD4 genome AF: 0.631 AC: 95851 AN: 152022 Hom.: 30741 Cov.: 32 AF XY: 0.636 AC XY: 47249 AN XY: 74296

Gnomad4 AFR AF: 0.552

Gnomad4 AMR AF: 0.641

Gnomad4 ASJ AF: 0.719

Gnomad4 EAS AF: 0.901

Gnomad4 SAS AF: 0.813

Gnomad4 FIN AF: 0.671

Gnomad4 NFE AF: 0.631

Gnomad4 OTH AF: 0.625

Alfa AF: 0.629 Hom.: 5153

Bravo AF: 0.621

Asia WGS AF: 0.840 AC: 2919 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	5.5
Dann	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs41750; hg19: chr7-116449000;