rs7143973

Variant names:

• chr14-41478625-T-C
• rs7143973
• ENST00000787890.1:n.53-10112T>C

Variant summary

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

The ENST00000787890.1(ENSG00000302567):​n.53-10112T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.366 in 151,962 control chromosomes in the GnomAD database, including 10,664 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 0.37 (10664 hom., cov: 32)
• Consequence: ENSG00000302567 ENST00000787890.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.739
• Publications: 1 publications found

Genes affected

ENSG00000302567 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.458 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000787890.1. 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
	ENSG00000302567	ENST00000787890.1		n.53-10112T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.366 AC: 55599 AN: 151846 Hom.: 10652 Cov.: 32

Gnomad AFR AF: 0.267

Gnomad AMI AF: 0.397

Gnomad AMR AF: 0.406

Gnomad ASJ AF: 0.316

Gnomad EAS AF: 0.474

Gnomad SAS AF: 0.335

Gnomad FIN AF: 0.433

Gnomad MID AF: 0.303

Gnomad NFE AF: 0.404

Gnomad OTH AF: 0.349

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

GnomAD4 genome AF: 0.366 AC: 55647 AN: 151962 Hom.: 10664 Cov.: 32 AF XY: 0.370 AC XY: 27489 AN XY: 74274

African (AFR) AF: 0.267 AC: 11067 AN: 41488

American (AMR) AF: 0.406 AC: 6194 AN: 15238

Ashkenazi Jewish (ASJ) AF: 0.316 AC: 1096 AN: 3470

East Asian (EAS) AF: 0.474 AC: 2447 AN: 5162

South Asian (SAS) AF: 0.336 AC: 1620 AN: 4816

European-Finnish (FIN) AF: 0.433 AC: 4577 AN: 10568

Middle Eastern (MID) AF: 0.308 AC: 90 AN: 292

European-Non Finnish (NFE) AF: 0.404 AC: 27463 AN: 67910

Other (OTH) AF: 0.347 AC: 732 AN: 2108

Alfa AF: 0.384 Hom.: 20627

Bravo AF: 0.361

Asia WGS AF: 0.417 AC: 1440 AN: 3452

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.49
DANN	Benign	0.49
PhyloP100		-0.74

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: rs7143973;

hg19: chr14-41947828;