chr7-41485018-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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107986787	XR_001745183.2	n.363-9690G>T		intron_variant	Intron 2 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

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 v4.3

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;