rs7613868

Variant names:

• chr3-124023182-C-T
• rs7613868
• ENST00000801819.1:n.81-9077C>T

Variant summary

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

The ENST00000801819.1(ENSG00000304291):​n.81-9077C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.445 in 151,934 control chromosomes in the GnomAD database, including 18,430 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 0.44 (18430 hom., cov: 31)
• Consequence: ENSG00000304291 ENST00000801819.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.528
• Publications: 1 publications found

Genes affected

ENSG00000304291 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.776 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
ENSG00000304291	ENST00000801819.1	n.81-9077C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.445 AC: 67501 AN: 151816 Hom.: 18383 Cov.: 31

Gnomad AFR AF: 0.783

Gnomad AMI AF: 0.351

Gnomad AMR AF: 0.373

Gnomad ASJ AF: 0.295

Gnomad EAS AF: 0.481

Gnomad SAS AF: 0.389

Gnomad FIN AF: 0.337

Gnomad MID AF: 0.351

Gnomad NFE AF: 0.283

Gnomad OTH AF: 0.422

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

GnomAD4 genome AF: 0.445 AC: 67598 AN: 151934 Hom.: 18430 Cov.: 31 AF XY: 0.445 AC XY: 33062 AN XY: 74256

African (AFR) AF: 0.784 AC: 32475 AN: 41442

American (AMR) AF: 0.372 AC: 5685 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.295 AC: 1023 AN: 3470

East Asian (EAS) AF: 0.481 AC: 2473 AN: 5146

South Asian (SAS) AF: 0.387 AC: 1857 AN: 4794

European-Finnish (FIN) AF: 0.337 AC: 3547 AN: 10528

Middle Eastern (MID) AF: 0.347 AC: 102 AN: 294

European-Non Finnish (NFE) AF: 0.283 AC: 19216 AN: 67970

Other (OTH) AF: 0.428 AC: 903 AN: 2112

Alfa AF: 0.396 Hom.: 5382

Bravo AF: 0.465

Asia WGS AF: 0.479 AC: 1664 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.33
DANN	Benign	0.45
PhyloP100		-0.53

Splicing

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

Other links and lift over

dbSNP: rs7613868; hg19: chr3-123742029;