14-35478408-C-T

Variant names:

• chr14-35478408-C-T
• rs10132268
• ENST00000848537.1:n.242-4052C>T

Variant summary

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

The ENST00000848537.1(ENSG00000310246):​n.242-4052C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.322 in 152,016 control chromosomes in the GnomAD database, including 8,762 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 0.32 (8762 hom., cov: 32)
• Consequence: ENSG00000310246 ENST00000848537.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.25
• Publications: 4 publications found

Genes affected

ENSG00000310246 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.522 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107984681	XR_001750713.2	n.122+3279C>T		intron_variant	Intron 1 of 1
LOC105370450	XR_943749.3	n.777-11G>A		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000310246	ENST00000848537.1	n.242-4052C>T		intron_variant	Intron 1 of 1
ENSG00000310272	ENST00000848660.1	n.103-11G>A		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.322 AC: 48904 AN: 151898 Hom.: 8750 Cov.: 32

Gnomad AFR AF: 0.457

Gnomad AMI AF: 0.135

Gnomad AMR AF: 0.224

Gnomad ASJ AF: 0.133

Gnomad EAS AF: 0.539

Gnomad SAS AF: 0.296

Gnomad FIN AF: 0.340

Gnomad MID AF: 0.180

Gnomad NFE AF: 0.257

Gnomad OTH AF: 0.305

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

GnomAD4 genome AF: 0.322 AC: 48963 AN: 152016 Hom.: 8762 Cov.: 32 AF XY: 0.324 AC XY: 24052 AN XY: 74310

African (AFR) AF: 0.457 AC: 18938 AN: 41434

American (AMR) AF: 0.225 AC: 3435 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.133 AC: 462 AN: 3468

East Asian (EAS) AF: 0.539 AC: 2788 AN: 5174

South Asian (SAS) AF: 0.295 AC: 1424 AN: 4824

European-Finnish (FIN) AF: 0.340 AC: 3586 AN: 10542

Middle Eastern (MID) AF: 0.173 AC: 51 AN: 294

European-Non Finnish (NFE) AF: 0.257 AC: 17497 AN: 67966

Other (OTH) AF: 0.312 AC: 659 AN: 2114

Alfa AF: 0.253 Hom.: 3958

Bravo AF: 0.320

Asia WGS AF: 0.432 AC: 1503 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.18
DANN	Benign	0.57
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs10132268; hg19: chr14-35947614;