2-184408401-C-T

Variant names:

• chr2-184408401-C-T
• rs1304514
• XR_001739819.1:n.319-24914C>T

Variant summary

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

The XR_001739819.1(LOC102724340):​n.319-24914C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.396 in 151,950 control chromosomes in the GnomAD database, including 14,303 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 0.40 (14303 hom., cov: 32)
• Consequence: LOC102724340 XR_001739819.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.933
• Publications: 3 publications found

Genes affected

LOC102724340 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.537 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC102724340	XR_001739819.1	n.319-24914C>T		intron_variant	Intron 3 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.396 AC: 60090 AN: 151832 Hom.: 14290 Cov.: 32

Gnomad AFR AF: 0.117

Gnomad AMI AF: 0.403

Gnomad AMR AF: 0.546

Gnomad ASJ AF: 0.452

Gnomad EAS AF: 0.532

Gnomad SAS AF: 0.424

Gnomad FIN AF: 0.454

Gnomad MID AF: 0.475

Gnomad NFE AF: 0.506

Gnomad OTH AF: 0.427

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

GnomAD4 genome AF: 0.396 AC: 60113 AN: 151950 Hom.: 14303 Cov.: 32 AF XY: 0.395 AC XY: 29343 AN XY: 74284

African (AFR) AF: 0.117 AC: 4854 AN: 41490

American (AMR) AF: 0.547 AC: 8328 AN: 15238

Ashkenazi Jewish (ASJ) AF: 0.452 AC: 1569 AN: 3468

East Asian (EAS) AF: 0.531 AC: 2737 AN: 5150

South Asian (SAS) AF: 0.425 AC: 2046 AN: 4818

European-Finnish (FIN) AF: 0.454 AC: 4791 AN: 10564

Middle Eastern (MID) AF: 0.473 AC: 138 AN: 292

European-Non Finnish (NFE) AF: 0.506 AC: 34373 AN: 67910

Other (OTH) AF: 0.431 AC: 910 AN: 2110

Alfa AF: 0.380 Hom.: 1837

Bravo AF: 0.396

Asia WGS AF: 0.475 AC: 1652 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.76
DANN	Benign	0.33
PhyloP100		-0.93

Splicing

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

Other links and lift over

dbSNP: rs1304514; hg19: chr2-185273128;