7-41485018-G-T

Variant names:

• chr7-41485018-G-T
• rs501002
• XR_001745183.2:n.363-9690G>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_001745183.2(LOC107986787):​n.363-9690G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. 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: LOC107986787 XR_001745183.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.257
• Publications: 0 publications found

Genes affected

LOC107986787 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.896 AC: 37184 AN: 41512

American (AMR) AF: 0.947 AC: 14488 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.941 AC: 3265 AN: 3470

East Asian (EAS) AF: 0.891 AC: 4618 AN: 5184

South Asian (SAS) AF: 0.926 AC: 4472 AN: 4830

European-Finnish (FIN) AF: 0.998 AC: 10586 AN: 10604

Middle Eastern (MID) AF: 0.904 AC: 264 AN: 292

European-Non Finnish (NFE) AF: 0.988 AC: 67218 AN: 68034

Other (OTH) AF: 0.945 AC: 1999 AN: 2116

Alfa AF: 0.976 Hom.: 29906

Bravo AF: 0.944

Asia WGS AF: 0.920 AC: 3195 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.023
DANN	Benign	0.27
PhyloP100		-0.26

Splicing

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

Other links and lift over

dbSNP: rs501002; hg19: chr7-41524616;