rs1951273

Variant names:

• chr14-35337763-T-C
• rs1951273
• ENST00000840468.1:n.188+2001A>G

Variant summary

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

The ENST00000840468.1(ENSG00000309352):​n.188+2001A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.288 in 152,176 control chromosomes in the GnomAD database, including 6,386 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 0.29 (6386 hom., cov: 32)
• Consequence: ENSG00000309352 ENST00000840468.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.11
• Publications: 6 publications found

Genes affected

ENSG00000309352 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.311 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000840468.1. 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
	ENSG00000309352	ENST00000840468.1		n.188+2001A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.288 AC: 43775 AN: 152058 Hom.: 6389 Cov.: 32

Gnomad AFR AF: 0.287

Gnomad AMI AF: 0.563

Gnomad AMR AF: 0.318

Gnomad ASJ AF: 0.203

Gnomad EAS AF: 0.195

Gnomad SAS AF: 0.243

Gnomad FIN AF: 0.336

Gnomad MID AF: 0.203

Gnomad NFE AF: 0.286

Gnomad OTH AF: 0.268

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

GnomAD4 genome AF: 0.288 AC: 43805 AN: 152176 Hom.: 6386 Cov.: 32 AF XY: 0.288 AC XY: 21450 AN XY: 74412

African (AFR) AF: 0.287 AC: 11895 AN: 41518

American (AMR) AF: 0.318 AC: 4861 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.203 AC: 704 AN: 3470

East Asian (EAS) AF: 0.195 AC: 1009 AN: 5164

South Asian (SAS) AF: 0.244 AC: 1178 AN: 4830

European-Finnish (FIN) AF: 0.336 AC: 3558 AN: 10598

Middle Eastern (MID) AF: 0.190 AC: 56 AN: 294

European-Non Finnish (NFE) AF: 0.286 AC: 19464 AN: 67990

Other (OTH) AF: 0.268 AC: 567 AN: 2114

Alfa AF: 0.294 Hom.: 2713

Bravo AF: 0.290

Asia WGS AF: 0.221 AC: 768 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.059
DANN	Benign	0.71
PhyloP100		-3.1

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: rs1951273;

hg19: chr14-35806969;