ENST00000848537.1:n.241+3178G>T

Variant names:

• chr14-35406565-G-T
• rs7157810
• ENST00000848537.1:n.241+3178G>T

Variant summary

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

The ENST00000848537.1(ENSG00000310246):​n.241+3178G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.193 in 152,118 control chromosomes in the GnomAD database, including 2,936 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 0.19 (2936 hom., cov: 33)
• Consequence: ENSG00000310246 ENST00000848537.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.375
• Publications: 3 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=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.209 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000310246	ENST00000848537.1		n.241+3178G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.193 AC: 29336 AN: 152000 Hom.: 2932 Cov.: 33

Gnomad AFR AF: 0.169

Gnomad AMI AF: 0.192

Gnomad AMR AF: 0.186

Gnomad ASJ AF: 0.188

Gnomad EAS AF: 0.123

Gnomad SAS AF: 0.181

Gnomad FIN AF: 0.218

Gnomad MID AF: 0.204

Gnomad NFE AF: 0.212

Gnomad OTH AF: 0.179

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

GnomAD4 genome AF: 0.193 AC: 29363 AN: 152118 Hom.: 2936 Cov.: 33 AF XY: 0.191 AC XY: 14174 AN XY: 74360

African (AFR) AF: 0.169 AC: 7015 AN: 41478

American (AMR) AF: 0.186 AC: 2843 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.188 AC: 654 AN: 3472

East Asian (EAS) AF: 0.123 AC: 639 AN: 5188

South Asian (SAS) AF: 0.181 AC: 871 AN: 4820

European-Finnish (FIN) AF: 0.218 AC: 2306 AN: 10556

Middle Eastern (MID) AF: 0.204 AC: 60 AN: 294

European-Non Finnish (NFE) AF: 0.212 AC: 14427 AN: 67998

Other (OTH) AF: 0.176 AC: 373 AN: 2114

Alfa AF: 0.150 Hom.: 524

Bravo AF: 0.191

Asia WGS AF: 0.155 AC: 542 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	1.1
DANN	Benign	0.71
PhyloP100		-0.38

Splicing

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

Other links and lift over

dbSNP: rs7157810; hg19: chr14-35875771;