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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000848537.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000310246	ENST00000848537.1		n.242-4052C>T		intron	N/A
	ENSG00000310272	ENST00000848660.1		n.103-11G>A		intron	N/A

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 v4.9

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs10132268;

hg19: chr14-35947614;