rs7146371

Variant names:

• chr14-71173972-T-C
• rs7146371
• ENST00000839854.1:n.370+7109A>G

Variant summary

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

The ENST00000839854.1(ENSG00000286423):​n.370+7109A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.62 in 152,028 control chromosomes in the GnomAD database, including 29,707 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 0.62 (29707 hom., cov: 32)
• Consequence: ENSG00000286423 ENST00000839854.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.90
• Publications: 8 publications found

Genes affected

ENSG00000286423 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.729 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000286423	ENST00000839854.1	n.370+7109A>G		intron_variant	Intron 2 of 2
ENSG00000286423	ENST00000839855.1	n.432+1740A>G		intron_variant	Intron 3 of 3
ENSG00000286423	ENST00000839856.1	n.576+7109A>G		intron_variant	Intron 3 of 3
ENSG00000286423	ENST00000839857.1	n.317+7109A>G		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.620 AC: 94216 AN: 151912 Hom.: 29676 Cov.: 32

Gnomad AFR AF: 0.735

Gnomad AMI AF: 0.739

Gnomad AMR AF: 0.569

Gnomad ASJ AF: 0.651

Gnomad EAS AF: 0.369

Gnomad SAS AF: 0.607

Gnomad FIN AF: 0.538

Gnomad MID AF: 0.750

Gnomad NFE AF: 0.591

Gnomad OTH AF: 0.616

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

GnomAD4 genome AF: 0.620 AC: 94295 AN: 152028 Hom.: 29707 Cov.: 32 AF XY: 0.615 AC XY: 45705 AN XY: 74290

African (AFR) AF: 0.736 AC: 30505 AN: 41466

American (AMR) AF: 0.569 AC: 8695 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.651 AC: 2259 AN: 3468

East Asian (EAS) AF: 0.369 AC: 1910 AN: 5176

South Asian (SAS) AF: 0.607 AC: 2928 AN: 4826

European-Finnish (FIN) AF: 0.538 AC: 5672 AN: 10534

Middle Eastern (MID) AF: 0.757 AC: 221 AN: 292

European-Non Finnish (NFE) AF: 0.591 AC: 40143 AN: 67960

Other (OTH) AF: 0.611 AC: 1288 AN: 2108

Alfa AF: 0.601 Hom.: 118547

Bravo AF: 0.627

Asia WGS AF: 0.489 AC: 1706 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.17
DANN	Benign	0.29
PhyloP100		-1.9

Splicing

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

Other links and lift over

dbSNP: rs7146371; hg19: chr14-71640689;