rs41750

Variant names:

• chr7-116808946-G-A
• rs41750

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 7 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.552 AC: 22877 AN: 41454

American (AMR) AF: 0.641 AC: 9799 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.719 AC: 2492 AN: 3464

East Asian (EAS) AF: 0.901 AC: 4666 AN: 5178

South Asian (SAS) AF: 0.813 AC: 3923 AN: 4824

European-Finnish (FIN) AF: 0.671 AC: 7084 AN: 10564

Middle Eastern (MID) AF: 0.636 AC: 187 AN: 294

European-Non Finnish (NFE) AF: 0.631 AC: 42858 AN: 67948

Other (OTH) AF: 0.625 AC: 1316 AN: 2106

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
PhyloP100		0.82

Splicing

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

Other links and lift over

dbSNP: rs41750; hg19: chr7-116449000;