14-46599121-T-G

Variant names:

• chr14-46599121-T-G
• rs1472242
• XR_001750753.1:n.814-1632A>C

Variant summary

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

The XR_001750753.1(LOC105370481):​n.814-1632A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.615 in 151,666 control chromosomes in the GnomAD database, including 28,929 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 0.62 (28929 hom., cov: 32)
• Consequence: LOC105370481 XR_001750753.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.195
• Publications: 1 publications found

Genes affected

LOC105370481 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.66).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.717 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105370481	XR_001750753.1	n.814-1632A>C		intron_variant	Intron 8 of 9
LOC105370481	XR_001750754.1	n.674-1632A>C		intron_variant	Intron 7 of 7
LOC105370481	XR_001750755.1	n.718-1632A>C		intron_variant	Intron 7 of 7
LOC105370481	XR_943828.2	n.814-1632A>C		intron_variant	Intron 8 of 8

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.615 AC: 93256 AN: 151548 Hom.: 28903 Cov.: 32

Gnomad AFR AF: 0.620

Gnomad AMI AF: 0.632

Gnomad AMR AF: 0.588

Gnomad ASJ AF: 0.480

Gnomad EAS AF: 0.736

Gnomad SAS AF: 0.563

Gnomad FIN AF: 0.721

Gnomad MID AF: 0.525

Gnomad NFE AF: 0.605

Gnomad OTH AF: 0.600

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

GnomAD4 genome AF: 0.615 AC: 93330 AN: 151666 Hom.: 28929 Cov.: 32 AF XY: 0.619 AC XY: 45870 AN XY: 74128

African (AFR) AF: 0.620 AC: 25652 AN: 41406

American (AMR) AF: 0.588 AC: 8944 AN: 15200

Ashkenazi Jewish (ASJ) AF: 0.480 AC: 1663 AN: 3466

East Asian (EAS) AF: 0.736 AC: 3785 AN: 5140

South Asian (SAS) AF: 0.562 AC: 2712 AN: 4828

European-Finnish (FIN) AF: 0.721 AC: 7625 AN: 10582

Middle Eastern (MID) AF: 0.527 AC: 155 AN: 294

European-Non Finnish (NFE) AF: 0.605 AC: 40962 AN: 67734

Other (OTH) AF: 0.597 AC: 1257 AN: 2106

Alfa AF: 0.598 Hom.: 15512

Bravo AF: 0.608

Asia WGS AF: 0.587 AC: 2036 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.66
CADD	Benign	12
DANN	Benign	0.81
PhyloP100		0.20

Splicing

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

Other links and lift over

dbSNP: rs1472242; hg19: chr14-47068324;