rs17150996

Positions:

• chr7-127534625-G-A
• chr7-127534625-G-C
• chr7-127534625-G-T

Variant summary

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

The XR_007060511.1(LOC105375490):​n.174+524C>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 0.291 in 151,948 control chromosomes in the GnomAD database, including 8,268 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 0.29 (8268 hom., cov: 31)
• Consequence: LOC105375490 XR_007060511.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.707

Genes affected

LOC105375490 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.707 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105375490	XR_007060511.1	n.174+524C>T		intron_variant, non_coding_transcript_variant
LOC105375490	XR_001745351.2	n.2291+524C>T		intron_variant, non_coding_transcript_variant
LOC105375490	XR_001745352.2	n.493+524C>T		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.291 AC: 44193 AN: 151830 Hom.: 8257 Cov.: 31

Gnomad AFR AF: 0.0811

Gnomad AMI AF: 0.355

Gnomad AMR AF: 0.335

Gnomad ASJ AF: 0.223

Gnomad EAS AF: 0.726

Gnomad SAS AF: 0.359

Gnomad FIN AF: 0.434

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.352

Gnomad OTH AF: 0.284

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

GnomAD4 genome AF: 0.291 AC: 44211 AN: 151948 Hom.: 8268 Cov.: 31 AF XY: 0.300 AC XY: 22292 AN XY: 74248

Gnomad4 AFR AF: 0.0811

Gnomad4 AMR AF: 0.335

Gnomad4 ASJ AF: 0.223

Gnomad4 EAS AF: 0.727

Gnomad4 SAS AF: 0.360

Gnomad4 FIN AF: 0.434

Gnomad4 NFE AF: 0.352

Gnomad4 OTH AF: 0.285

Alfa AF: 0.317 Hom.: 1087

Bravo AF: 0.275

Asia WGS AF: 0.483 AC: 1674 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.58
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17150996; hg19: chr7-127174679;