chr2-31666502-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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107985862	XR_001739385.2	n.541C>T		non_coding_transcript_exon_variant	Exon 6 of 6
LOC107985862	XR_001739386.2	n.498C>T		non_coding_transcript_exon_variant	Exon 6 of 6
LOC107985862	XR_001739387.1	n.541C>T		non_coding_transcript_exon_variant	Exon 6 of 7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000306342	ENST00000817056.1	n.281-3493C>T		intron_variant	Intron 2 of 4

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 v4.3

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;