7-41485018-G-T

Position:

• chr7-41485018-G-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 0.952 in 152,248 control chromosomes in the GnomAD database, including 69,208 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 0.95 (69208 hom., cov: 33)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.257

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.982 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.41485018G>T		intergenic_region
LOC107986787	XR_001745183.2	n.363-9690G>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.953 AC: 144911 AN: 152130 Hom.: 69172 Cov.: 33

Gnomad AFR AF: 0.896

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.947

Gnomad ASJ AF: 0.941

Gnomad EAS AF: 0.891

Gnomad SAS AF: 0.926

Gnomad FIN AF: 0.998

Gnomad MID AF: 0.898

Gnomad NFE AF: 0.988

Gnomad OTH AF: 0.945

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

GnomAD4 genome AF: 0.952 AC: 145006 AN: 152248 Hom.: 69208 Cov.: 33 AF XY: 0.951 AC XY: 70801 AN XY: 74436

Gnomad4 AFR AF: 0.896

Gnomad4 AMR AF: 0.947

Gnomad4 ASJ AF: 0.941

Gnomad4 EAS AF: 0.891

Gnomad4 SAS AF: 0.926

Gnomad4 FIN AF: 0.998

Gnomad4 NFE AF: 0.988

Gnomad4 OTH AF: 0.945

Alfa AF: 0.977 Hom.: 25875

Bravo AF: 0.944

Asia WGS AF: 0.920 AC: 3195 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.023
DANN	Benign	0.27

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs501002; hg19: chr7-41524616;