rs1160277

chr7-134620565-C-T

Variant summary

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

The XR_007060537.1(LOC124901750):n.29222-617G>A 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 0.246 in 152,086 control chromosomes in the GnomAD database, including 5,426 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 0.25 (5426 hom., cov: 32)
• Consequence: LOC124901750 XR_007060537.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.168

Genes affected

LOC124901750 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.319 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124901750	XR_007060537.1	n.29222-617G>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.246 AC: 37360 AN: 151968 Hom.: 5418 Cov.: 32

Gnomad AFR AF: 0.0825

Gnomad AMI AF: 0.328

Gnomad AMR AF: 0.274

Gnomad ASJ AF: 0.279

Gnomad EAS AF: 0.295

Gnomad SAS AF: 0.266

Gnomad FIN AF: 0.298

Gnomad MID AF: 0.228

Gnomad NFE AF: 0.323

Gnomad OTH AF: 0.248

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

GnomAD4 genome AF: 0.246 AC: 37380 AN: 152086 Hom.: 5426 Cov.: 32 AF XY: 0.246 AC XY: 18283 AN XY: 74348

Gnomad4 AFR AF: 0.0824

Gnomad4 AMR AF: 0.274

Gnomad4 ASJ AF: 0.279

Gnomad4 EAS AF: 0.295

Gnomad4 SAS AF: 0.267

Gnomad4 FIN AF: 0.298

Gnomad4 NFE AF: 0.323

Gnomad4 OTH AF: 0.252

Alfa AF: 0.275 Hom.: 797

Bravo AF: 0.241

Asia WGS AF: 0.284 AC: 988 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	4.8
Dann	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1160277; hg19: chr7-134305317;