2-31666502-G-A

Variant names:

• chr2-31666502-G-A
• rs13027103
• XR_001739385.2:n.541C>T

Variant summary

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

The XR_001739385.2(LOC107985862):​n.541C>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 0.101 in 152,094 control chromosomes in the GnomAD database, including 811 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 0.10 (811 hom., cov: 31)
• Consequence: LOC107985862 XR_001739385.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.60
• Publications: 5 publications found

Genes affected

LOC107985862 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.109 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000817056.1. 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
	ENSG00000306342	ENST00000817056.1		n.281-3493C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.101 AC: 15363 AN: 151976 Hom.: 801 Cov.: 31

Gnomad AFR AF: 0.111

Gnomad AMI AF: 0.0800

Gnomad AMR AF: 0.0796

Gnomad ASJ AF: 0.178

Gnomad EAS AF: 0.0883

Gnomad SAS AF: 0.0840

Gnomad FIN AF: 0.0988

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.0981

Gnomad OTH AF: 0.110

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

GnomAD4 genome AF: 0.101 AC: 15399 AN: 152094 Hom.: 811 Cov.: 31 AF XY: 0.101 AC XY: 7495 AN XY: 74364

African (AFR) AF: 0.112 AC: 4638 AN: 41486

American (AMR) AF: 0.0796 AC: 1215 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.178 AC: 617 AN: 3470

East Asian (EAS) AF: 0.0881 AC: 454 AN: 5152

South Asian (SAS) AF: 0.0846 AC: 408 AN: 4820

European-Finnish (FIN) AF: 0.0988 AC: 1048 AN: 10606

Middle Eastern (MID) AF: 0.150 AC: 44 AN: 294

European-Non Finnish (NFE) AF: 0.0981 AC: 6669 AN: 67978

Other (OTH) AF: 0.110 AC: 233 AN: 2110

Alfa AF: 0.104 Hom.: 1178

Bravo AF: 0.101

Asia WGS AF: 0.0920 AC: 319 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	0.41
DANN	Benign	0.74
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs13027103; hg19: chr2-31891571;