5-67949675-G-T

Variant names:

• chr5-67949675-G-T
• rs10078620
• XR_002956213.2:n.1040G>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_002956213.2(LOC105379007):​n.1040G>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_002956213.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.84
• Publications: 1 publications found

Genes affected

LOC105379007 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
LOC105379007	XR_002956213.2	n.1040G>T		non_coding_transcript_exon_variant	Exon 3 of 3
LOC105379007	XR_948392.3	n.1235G>T		non_coding_transcript_exon_variant	Exon 4 of 4
LOC107986420	XR_001742692.1	n.147-5540C>A		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000302346	ENST00000785994.1	n.271-5540C>A		intron_variant	Intron 3 of 5
ENSG00000302346	ENST00000785995.1	n.304-5540C>A		intron_variant	Intron 3 of 4

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

African (AFR) AF: 0.135 AC: 5584 AN: 41242

American (AMR) AF: 0.129 AC: 1965 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.143 AC: 493 AN: 3458

East Asian (EAS) AF: 0.0243 AC: 125 AN: 5148

South Asian (SAS) AF: 0.101 AC: 485 AN: 4798

European-Finnish (FIN) AF: 0.297 AC: 3093 AN: 10408

Middle Eastern (MID) AF: 0.161 AC: 47 AN: 292

European-Non Finnish (NFE) AF: 0.231 AC: 15653 AN: 67880

Other (OTH) AF: 0.175 AC: 367 AN: 2100

Alfa AF: 0.132 Hom.: 313

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
PhyloP100		-3.8

Splicing

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

Other links and lift over

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