14-97036408-G-C

Variant names:

• chr14-97036408-G-C
• rs1683119
• XR_944180.4:n.284+8410G>C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_944180.4(LOC105370647):​n.284+8410G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.78 in 152,124 control chromosomes in the GnomAD database, including 47,060 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 0.78 (47060 hom., cov: 32)
• Consequence: LOC105370647 XR_944180.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.64

Genes affected

LOC105370647 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.974 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105370647	XR_944180.4	n.284+8410G>C		intron_variant	Intron 1 of 2

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.779 AC: 118470 AN: 152006 Hom.: 47002 Cov.: 32

Gnomad AFR AF: 0.901

Gnomad AMI AF: 0.662

Gnomad AMR AF: 0.798

Gnomad ASJ AF: 0.716

Gnomad EAS AF: 0.997

Gnomad SAS AF: 0.887

Gnomad FIN AF: 0.711

Gnomad MID AF: 0.725

Gnomad NFE AF: 0.693

Gnomad OTH AF: 0.758

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

GnomAD4 genome AF: 0.780 AC: 118586 AN: 152124 Hom.: 47060 Cov.: 32 AF XY: 0.783 AC XY: 58198 AN XY: 74346

Gnomad4 AFR AF: 0.901

Gnomad4 AMR AF: 0.798

Gnomad4 ASJ AF: 0.716

Gnomad4 EAS AF: 0.997

Gnomad4 SAS AF: 0.887

Gnomad4 FIN AF: 0.711

Gnomad4 NFE AF: 0.693

Gnomad4 OTH AF: 0.760

Alfa AF: 0.643 Hom.: 2037

Bravo AF: 0.790

Asia WGS AF: 0.934 AC: 3246 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.12
DANN	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1683119; hg19: chr14-97502745;