rs7716959

chr5-173506839-G-Achr5-173506839-G-C

Variant summary

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

The XR_001743001.1(LOC105377732):n.2862+467G>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 0.366 in 151,842 control chromosomes in the GnomAD database, including 10,435 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 0.37 (10435 hom., cov: 31)
• Consequence: LOC105377732 XR_001743001.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.290

Genes affected

LOC105377732 (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 (AMR) allele frequency at 95% confidence interval = 0.455 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105377732	XR_001743001.1	n.2862+467G>A		intron_variant, non_coding_transcript_variant
LOC105377732	XR_007059057.1	n.3922+467G>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.366 AC: 55572 AN: 151724 Hom.: 10412 Cov.: 31

Gnomad AFR AF: 0.294

Gnomad AMI AF: 0.434

Gnomad AMR AF: 0.463

Gnomad ASJ AF: 0.329

Gnomad EAS AF: 0.272

Gnomad SAS AF: 0.402

Gnomad FIN AF: 0.389

Gnomad MID AF: 0.323

Gnomad NFE AF: 0.390

Gnomad OTH AF: 0.389

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

GnomAD4 genome AF: 0.366 AC: 55641 AN: 151842 Hom.: 10435 Cov.: 31 AF XY: 0.370 AC XY: 27452 AN XY: 74220

Gnomad4 AFR AF: 0.294

Gnomad4 AMR AF: 0.464

Gnomad4 ASJ AF: 0.329

Gnomad4 EAS AF: 0.272

Gnomad4 SAS AF: 0.403

Gnomad4 FIN AF: 0.389

Gnomad4 NFE AF: 0.390

Gnomad4 OTH AF: 0.394

Alfa AF: 0.391 Hom.: 5918

Bravo AF: 0.368

Asia WGS AF: 0.347 AC: 1209 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	3.7
Dann	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7716959; hg19: chr5-172933842; COSMIC: COSV60232066;