rs17598306

Positions:

• chr7-96952499-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_007060444.1(LOC124901703):​n.31-4538C>T variant causes a intron, non coding transcript 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, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.522

Genes affected

LOC124901703 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124901703	XR_007060444.1	n.31-4538C>T		intron_variant, non_coding_transcript_variant

Ensembl

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

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

Gnomad4 AFR AF: 0.0958

Gnomad4 AMR AF: 0.0695

Gnomad4 ASJ AF: 0.118

Gnomad4 EAS AF: 0.000963

Gnomad4 SAS AF: 0.135

Gnomad4 FIN AF: 0.0810

Gnomad4 NFE AF: 0.134

Gnomad4 OTH AF: 0.106

Alfa AF: 0.126 Hom.: 1573

Bravo AF: 0.105

Asia WGS AF: 0.0530 AC: 185 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17598306; hg19: chr7-96581811;