chr14-35421655-A-G

Variant names:

• chr14-35421655-A-G
• rs762009
• ENST00000848537.1:n.241+18268A>G

Variant summary

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

The ENST00000848537.1(ENSG00000310246):​n.241+18268A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.718 in 152,104 control chromosomes in the GnomAD database, including 39,496 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 0.72 (39496 hom., cov: 31)
• Consequence: ENSG00000310246 ENST00000848537.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.350
• 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=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.756 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+18268A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.718 AC: 109150 AN: 151986 Hom.: 39455 Cov.: 31

Gnomad AFR AF: 0.763

Gnomad AMI AF: 0.631

Gnomad AMR AF: 0.610

Gnomad ASJ AF: 0.717

Gnomad EAS AF: 0.631

Gnomad SAS AF: 0.666

Gnomad FIN AF: 0.705

Gnomad MID AF: 0.652

Gnomad NFE AF: 0.730

Gnomad OTH AF: 0.696

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

GnomAD4 genome AF: 0.718 AC: 109242 AN: 152104 Hom.: 39496 Cov.: 31 AF XY: 0.714 AC XY: 53081 AN XY: 74334

African (AFR) AF: 0.763 AC: 31672 AN: 41510

American (AMR) AF: 0.609 AC: 9303 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.717 AC: 2485 AN: 3468

East Asian (EAS) AF: 0.631 AC: 3268 AN: 5178

South Asian (SAS) AF: 0.664 AC: 3190 AN: 4804

European-Finnish (FIN) AF: 0.705 AC: 7456 AN: 10578

Middle Eastern (MID) AF: 0.656 AC: 193 AN: 294

European-Non Finnish (NFE) AF: 0.730 AC: 49628 AN: 67986

Other (OTH) AF: 0.699 AC: 1473 AN: 2108

Alfa AF: 0.724 Hom.: 31567

Bravo AF: 0.711

Asia WGS AF: 0.639 AC: 2226 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.1
DANN	Benign	0.80
PhyloP100		-0.35

Splicing

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

Other links and lift over

dbSNP: rs762009; hg19: chr14-35890861;