rs3763486

Positions:

• chr7-151026178-T-C

Variant summary

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

The XR_007060593.1(LOC124901777):​n.502+629A>G 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 0.227 in 152,102 control chromosomes in the GnomAD database, including 4,349 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 0.23 (4349 hom., cov: 32)
• Consequence: LOC124901777 XR_007060593.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.03

Genes affected

LOC124901777 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.444 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC124901777	XR_007060593.1	n.502+629A>G		intron_variant, non_coding_transcript_variant
LOC124901777	XR_007060594.1	n.502+629A>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.227 AC: 34542 AN: 151984 Hom.: 4333 Cov.: 32

Gnomad AFR AF: 0.248

Gnomad AMI AF: 0.105

Gnomad AMR AF: 0.360

Gnomad ASJ AF: 0.165

Gnomad EAS AF: 0.460

Gnomad SAS AF: 0.140

Gnomad FIN AF: 0.221

Gnomad MID AF: 0.231

Gnomad NFE AF: 0.179

Gnomad OTH AF: 0.234

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

GnomAD4 genome AF: 0.227 AC: 34578 AN: 152102 Hom.: 4349 Cov.: 32 AF XY: 0.231 AC XY: 17177 AN XY: 74362

Gnomad4 AFR AF: 0.248

Gnomad4 AMR AF: 0.361

Gnomad4 ASJ AF: 0.165

Gnomad4 EAS AF: 0.460

Gnomad4 SAS AF: 0.141

Gnomad4 FIN AF: 0.221

Gnomad4 NFE AF: 0.179

Gnomad4 OTH AF: 0.231

Alfa AF: 0.203 Hom.: 3705

Bravo AF: 0.248

Asia WGS AF: 0.281 AC: 977 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.15
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3763486; hg19: chr7-150723265;