2-122379314-C-T

Variant names:

• chr2-122379314-C-T
• rs1919922
• ENST00000657880.2:n.756-153537C>T

Variant summary

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

The ENST00000657880.2(ENSG00000286481):​n.756-153537C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.157 in 152,100 control chromosomes in the GnomAD database, including 2,381 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 0.16 (2381 hom., cov: 32)
• Consequence: ENSG00000286481 ENST00000657880.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.125
• Publications: 4 publications found

Genes affected

ENSG00000286481 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.446 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105373592	XR_001739684.2	n.753-13649C>T		intron_variant	Intron 3 of 6
LOC105373592	XR_007087222.1	n.753-13649C>T		intron_variant	Intron 3 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000286481	ENST00000657880.2	n.756-153537C>T		intron_variant	Intron 3 of 8
ENSG00000286481	ENST00000819524.1	n.102-13649C>T		intron_variant	Intron 1 of 2
ENSG00000286481	ENST00000819525.1	n.169-13649C>T		intron_variant	Intron 1 of 2
ENSG00000286481	ENST00000819526.1	n.122-13649C>T		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.157 AC: 23820 AN: 151982 Hom.: 2370 Cov.: 32

Gnomad AFR AF: 0.161

Gnomad AMI AF: 0.143

Gnomad AMR AF: 0.242

Gnomad ASJ AF: 0.177

Gnomad EAS AF: 0.460

Gnomad SAS AF: 0.226

Gnomad FIN AF: 0.127

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.111

Gnomad OTH AF: 0.165

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

GnomAD4 genome AF: 0.157 AC: 23863 AN: 152100 Hom.: 2381 Cov.: 32 AF XY: 0.161 AC XY: 11949 AN XY: 74368

African (AFR) AF: 0.161 AC: 6672 AN: 41480

American (AMR) AF: 0.242 AC: 3702 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.177 AC: 614 AN: 3468

East Asian (EAS) AF: 0.461 AC: 2373 AN: 5148

South Asian (SAS) AF: 0.226 AC: 1088 AN: 4812

European-Finnish (FIN) AF: 0.127 AC: 1343 AN: 10576

Middle Eastern (MID) AF: 0.163 AC: 48 AN: 294

European-Non Finnish (NFE) AF: 0.111 AC: 7530 AN: 68016

Other (OTH) AF: 0.172 AC: 363 AN: 2112

Alfa AF: 0.129 Hom.: 2868

Bravo AF: 0.170

Asia WGS AF: 0.357 AC: 1241 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.0
DANN	Benign	0.54
PhyloP100		-0.13

Splicing

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

Other links and lift over

dbSNP: rs1919922; hg19: chr2-123136890;