XR_002956213.2:n.1040G>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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000785994.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000302346	ENST00000785994.1		n.271-5540C>A		intron	N/A
	ENSG00000302346	ENST00000785995.1		n.304-5540C>A		intron	N/A

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 v4.9

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;