XR_001750926.1:n.212-565G>A

Variant names:

• chr14-40443243-G-A
• rs2415603
• XR_001750926.1:n.212-565G>A

Variant summary

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

The XR_001750926.1(LOC105370465):​n.212-565G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.952 in 151,952 control chromosomes in the GnomAD database, including 68,927 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 0.95 (68927 hom., cov: 30)
• Consequence: LOC105370465 XR_001750926.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.342
• Publications: 2 publications found

Genes affected

LOC105370465 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.979 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105370465	XR_001750926.1	n.212-565G>A		intron_variant	Intron 1 of 2

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.952 AC: 144555 AN: 151834 Hom.: 68870 Cov.: 30

Gnomad AFR AF: 0.987

Gnomad AMI AF: 0.876

Gnomad AMR AF: 0.965

Gnomad ASJ AF: 0.953

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.988

Gnomad FIN AF: 0.917

Gnomad MID AF: 0.968

Gnomad NFE AF: 0.928

Gnomad OTH AF: 0.958

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

GnomAD4 genome AF: 0.952 AC: 144671 AN: 151952 Hom.: 68927 Cov.: 30 AF XY: 0.953 AC XY: 70719 AN XY: 74238

African (AFR) AF: 0.987 AC: 40952 AN: 41508

American (AMR) AF: 0.965 AC: 14703 AN: 15232

Ashkenazi Jewish (ASJ) AF: 0.953 AC: 3305 AN: 3468

East Asian (EAS) AF: 1.00 AC: 5135 AN: 5136

South Asian (SAS) AF: 0.988 AC: 4766 AN: 4824

European-Finnish (FIN) AF: 0.917 AC: 9654 AN: 10528

Middle Eastern (MID) AF: 0.966 AC: 284 AN: 294

European-Non Finnish (NFE) AF: 0.928 AC: 63057 AN: 67946

Other (OTH) AF: 0.958 AC: 2018 AN: 2106

Alfa AF: 0.938 Hom.: 34214

Bravo AF: 0.956

Asia WGS AF: 0.990 AC: 3427 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.45
DANN	Benign	0.34
PhyloP100		-0.34

Splicing

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

Other links and lift over

dbSNP: rs2415603; hg19: chr14-40912447;