14-97776606-G-C

Variant names:

• chr14-97776606-G-C
• rs716308
• XR_944186.4:n.503+2524G>C

Variant summary

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

The XR_944186.4(LOC105370651):​n.503+2524G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.61 in 151,854 control chromosomes in the GnomAD database, including 28,773 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 0.61 (28773 hom., cov: 31)
• Consequence: LOC105370651 XR_944186.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.144
• Publications: 1 publications found

Genes affected

LOC105370651 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.902 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105370651	XR_944186.4	n.503+2524G>C		intron_variant	Intron 3 of 4

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.610 AC: 92506 AN: 151738 Hom.: 28752 Cov.: 31

Gnomad AFR AF: 0.538

Gnomad AMI AF: 0.626

Gnomad AMR AF: 0.714

Gnomad ASJ AF: 0.675

Gnomad EAS AF: 0.925

Gnomad SAS AF: 0.677

Gnomad FIN AF: 0.591

Gnomad MID AF: 0.675

Gnomad NFE AF: 0.599

Gnomad OTH AF: 0.637

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

GnomAD4 genome AF: 0.610 AC: 92574 AN: 151854 Hom.: 28773 Cov.: 31 AF XY: 0.614 AC XY: 45576 AN XY: 74196

African (AFR) AF: 0.538 AC: 22255 AN: 41396

American (AMR) AF: 0.715 AC: 10921 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.675 AC: 2340 AN: 3468

East Asian (EAS) AF: 0.924 AC: 4742 AN: 5130

South Asian (SAS) AF: 0.676 AC: 3258 AN: 4818

European-Finnish (FIN) AF: 0.591 AC: 6225 AN: 10532

Middle Eastern (MID) AF: 0.682 AC: 199 AN: 292

European-Non Finnish (NFE) AF: 0.599 AC: 40713 AN: 67918

Other (OTH) AF: 0.641 AC: 1351 AN: 2106

Alfa AF: 0.494 Hom.: 1468

Bravo AF: 0.617

Asia WGS AF: 0.759 AC: 2635 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.4
DANN	Benign	0.33
PhyloP100		-0.14

Splicing

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

Other links and lift over

dbSNP: rs716308; hg19: chr14-98242943;