chr7-96952499-C-T

Variant names:

• chr7-96952499-C-T
• rs17598306
• XR_007060444.1:n.31-4538C>T

Variant summary

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

The XR_007060444.1(LOC124901703):​n.31-4538C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.108 in 152,240 control chromosomes in the GnomAD database, including 1,007 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 0.11 (1007 hom., cov: 32)
• Consequence: LOC124901703 XR_007060444.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.522
• Publications: 8 publications found

Genes affected

LOC124901703 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.132 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.108 AC: 16440 AN: 152122 Hom.: 1007 Cov.: 32

Gnomad AFR AF: 0.0961

Gnomad AMI AF: 0.0855

Gnomad AMR AF: 0.0698

Gnomad ASJ AF: 0.118

Gnomad EAS AF: 0.000961

Gnomad SAS AF: 0.135

Gnomad FIN AF: 0.0810

Gnomad MID AF: 0.156

Gnomad NFE AF: 0.134

Gnomad OTH AF: 0.108

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

GnomAD4 genome AF: 0.108 AC: 16436 AN: 152240 Hom.: 1007 Cov.: 32 AF XY: 0.103 AC XY: 7649 AN XY: 74446

African (AFR) AF: 0.0958 AC: 3980 AN: 41534

American (AMR) AF: 0.0695 AC: 1064 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.118 AC: 409 AN: 3468

East Asian (EAS) AF: 0.000963 AC: 5 AN: 5190

South Asian (SAS) AF: 0.135 AC: 651 AN: 4826

European-Finnish (FIN) AF: 0.0810 AC: 859 AN: 10608

Middle Eastern (MID) AF: 0.154 AC: 45 AN: 292

European-Non Finnish (NFE) AF: 0.134 AC: 9120 AN: 67994

Other (OTH) AF: 0.106 AC: 225 AN: 2114

Alfa AF: 0.123 Hom.: 2260

Bravo AF: 0.105

Asia WGS AF: 0.0530 AC: 185 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	10
DANN	Benign	0.47
PhyloP100		0.52

Splicing

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

Other links and lift over

dbSNP: rs17598306; hg19: chr7-96581811;