rs2524976

chr7-96428028-T-C

Variant summary

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

The XR_001745288.2(LOC105375410):n.869-650T>C 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 0.322 in 152,102 control chromosomes in the GnomAD database, including 8,171 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 0.32 (8171 hom., cov: 32)
• Consequence: LOC105375410 XR_001745288.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.548

Genes affected

LOC105375410 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.345 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105375410	XR_001745288.2	n.869-650T>C		intron_variant, non_coding_transcript_variant
LOC105375410	XR_927777.3	n.837-650T>C		intron_variant, non_coding_transcript_variant
LOC105375410	XR_927779.3	n.836+5613T>C		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.322 AC: 48937 AN: 151984 Hom.: 8166 Cov.: 32

Gnomad AFR AF: 0.334

Gnomad AMI AF: 0.324

Gnomad AMR AF: 0.264

Gnomad ASJ AF: 0.321

Gnomad EAS AF: 0.0484

Gnomad SAS AF: 0.228

Gnomad FIN AF: 0.366

Gnomad MID AF: 0.326

Gnomad NFE AF: 0.348

Gnomad OTH AF: 0.320

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

GnomAD4 genome AF: 0.322 AC: 48974 AN: 152102 Hom.: 8171 Cov.: 32 AF XY: 0.317 AC XY: 23564 AN XY: 74364

Gnomad4 AFR AF: 0.334

Gnomad4 AMR AF: 0.263

Gnomad4 ASJ AF: 0.321

Gnomad4 EAS AF: 0.0485

Gnomad4 SAS AF: 0.230

Gnomad4 FIN AF: 0.366

Gnomad4 NFE AF: 0.348

Gnomad4 OTH AF: 0.316

Alfa AF: 0.328 Hom.: 2085

Bravo AF: 0.317

Asia WGS AF: 0.145 AC: 505 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	0.49
Dann	Benign	0.22

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2524976; hg19: chr7-96057340;