5-67949675-G-T

Position:

• chr5-67949675-G-T

Variant summary

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

The XR_948392.3(LOC105379007):​n.1235G>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.185 in 151,478 control chromosomes in the GnomAD database, including 2,921 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 0.19 (2921 hom., cov: 32)
• Consequence: LOC105379007 XR_948392.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.84

Genes affected

LOC105379007 (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 (NFE) allele frequency at 95% confidence interval = 0.228 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105379007	XR_002956213.2	n.1040G>T		non_coding_transcript_exon_variant	3/3
LOC105379007	XR_948392.3	n.1235G>T		non_coding_transcript_exon_variant	4/4
		n.67949675G>T		intergenic_region
LOC107986420	XR_001742692.1	n.147-5540C>A		intron_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.185 AC: 28026 AN: 151360 Hom.: 2922 Cov.: 32

Gnomad AFR AF: 0.136

Gnomad AMI AF: 0.240

Gnomad AMR AF: 0.129

Gnomad ASJ AF: 0.143

Gnomad EAS AF: 0.0246

Gnomad SAS AF: 0.101

Gnomad FIN AF: 0.297

Gnomad MID AF: 0.153

Gnomad NFE AF: 0.231

Gnomad OTH AF: 0.176

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

GnomAD4 genome AF: 0.185 AC: 28030 AN: 151478 Hom.: 2921 Cov.: 32 AF XY: 0.184 AC XY: 13637 AN XY: 73986

Gnomad4 AFR AF: 0.135

Gnomad4 AMR AF: 0.129

Gnomad4 ASJ AF: 0.143

Gnomad4 EAS AF: 0.0243

Gnomad4 SAS AF: 0.101

Gnomad4 FIN AF: 0.297

Gnomad4 NFE AF: 0.231

Gnomad4 OTH AF: 0.175

Alfa AF: 0.132 Hom.: 305

Bravo AF: 0.168

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.14
DANN	Benign	0.12

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10078620; hg19: chr5-67245503; COSMIC: COSV56538979;