rs2415603

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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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 v4.9

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;