2-42919660-T-C

Variant names:

• chr2-42919660-T-C
• rs1078100
• XR_940014.3:n.2132A>G

Variant summary

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

The XR_940014.3(LOC105374568):​n.2132A>G 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 0.646 in 152,080 control chromosomes in the GnomAD database, including 32,605 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 0.65 (32605 hom., cov: 32)
• Consequence: LOC105374568 XR_940014.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.547
• Publications: 6 publications found

Genes affected

LOC105374568 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.762 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105374568	XR_940014.3	n.2132A>G		non_coding_transcript_exon_variant	Exon 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000307331	ENST00000825116.1	n.838-14041T>C		intron_variant	Intron 1 of 2
ENSG00000307331	ENST00000825118.1	n.111-232T>C		intron_variant	Intron 1 of 5
ENSG00000307331	ENST00000825119.1	n.102-232T>C		intron_variant	Intron 1 of 4
ENSG00000307331	ENST00000825120.1	n.105+1881T>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.646 AC: 98202 AN: 151962 Hom.: 32553 Cov.: 32

Gnomad AFR AF: 0.769

Gnomad AMI AF: 0.388

Gnomad AMR AF: 0.728

Gnomad ASJ AF: 0.661

Gnomad EAS AF: 0.650

Gnomad SAS AF: 0.748

Gnomad FIN AF: 0.558

Gnomad MID AF: 0.804

Gnomad NFE AF: 0.561

Gnomad OTH AF: 0.660

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

GnomAD4 genome AF: 0.646 AC: 98312 AN: 152080 Hom.: 32605 Cov.: 32 AF XY: 0.649 AC XY: 48251 AN XY: 74352

African (AFR) AF: 0.769 AC: 31892 AN: 41480

American (AMR) AF: 0.728 AC: 11135 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.661 AC: 2291 AN: 3468

East Asian (EAS) AF: 0.651 AC: 3361 AN: 5164

South Asian (SAS) AF: 0.748 AC: 3607 AN: 4820

European-Finnish (FIN) AF: 0.558 AC: 5897 AN: 10570

Middle Eastern (MID) AF: 0.806 AC: 237 AN: 294

European-Non Finnish (NFE) AF: 0.561 AC: 38138 AN: 67972

Other (OTH) AF: 0.664 AC: 1401 AN: 2110

Alfa AF: 0.599 Hom.: 51138

Bravo AF: 0.666

Asia WGS AF: 0.744 AC: 2587 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	3.2
DANN	Benign	0.58
PhyloP100		-0.55

Splicing

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

Other links and lift over

dbSNP: rs1078100; hg19: chr2-43146800;