14-97727875-C-T

Variant names:

• chr14-97727875-C-T
• rs1462256
• ENST00000775600.1:n.351+19900C>T

Variant summary

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

The ENST00000775600.1(ENSG00000301019):​n.351+19900C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.468 in 151,912 control chromosomes in the GnomAD database, including 17,098 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 0.47 (17098 hom., cov: 31)
• Consequence: ENSG00000301019 ENST00000775600.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.787
• Publications: 8 publications found

Genes affected

ENSG00000301019 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.579 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105370651	XR_944186.4	n.349+19900C>T		intron_variant	Intron 2 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000301019	ENST00000775600.1	n.351+19900C>T		intron_variant	Intron 2 of 3
ENSG00000301019	ENST00000775601.1	n.349+19900C>T		intron_variant	Intron 2 of 2
ENSG00000301019	ENST00000775602.1	n.448+11526C>T		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.468 AC: 70996 AN: 151794 Hom.: 17087 Cov.: 31

Gnomad AFR AF: 0.585

Gnomad AMI AF: 0.340

Gnomad AMR AF: 0.513

Gnomad ASJ AF: 0.452

Gnomad EAS AF: 0.317

Gnomad SAS AF: 0.426

Gnomad FIN AF: 0.393

Gnomad MID AF: 0.339

Gnomad NFE AF: 0.416

Gnomad OTH AF: 0.453

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

GnomAD4 genome AF: 0.468 AC: 71054 AN: 151912 Hom.: 17098 Cov.: 31 AF XY: 0.466 AC XY: 34625 AN XY: 74240

African (AFR) AF: 0.585 AC: 24224 AN: 41402

American (AMR) AF: 0.513 AC: 7835 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.452 AC: 1570 AN: 3472

East Asian (EAS) AF: 0.316 AC: 1626 AN: 5144

South Asian (SAS) AF: 0.426 AC: 2051 AN: 4816

European-Finnish (FIN) AF: 0.393 AC: 4153 AN: 10558

Middle Eastern (MID) AF: 0.337 AC: 99 AN: 294

European-Non Finnish (NFE) AF: 0.416 AC: 28234 AN: 67944

Other (OTH) AF: 0.452 AC: 953 AN: 2110

Alfa AF: 0.432 Hom.: 60784

Bravo AF: 0.480

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.017
DANN	Benign	0.50
PhyloP100		-0.79

Splicing

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

Other links and lift over

dbSNP: rs1462256; hg19: chr14-98194212;