rs7185124

Variant names:

• chr16-13656837-T-C
• rs7185124
• ENST00000727119.1:n.213-7586A>G

Variant summary

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

The ENST00000727119.1(ENSG00000294970):​n.213-7586A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.781 in 152,178 control chromosomes in the GnomAD database, including 46,540 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 0.78 (46540 hom., cov: 33)
• Consequence: ENSG00000294970 ENST00000727119.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.302
• Publications: 6 publications found

Genes affected

ENSG00000294970 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.865 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
ENSG00000294970	ENST00000727119.1	n.213-7586A>G		intron_variant	Intron 1 of 1
ENSG00000294970	ENST00000727120.1	n.309-7586A>G		intron_variant	Intron 2 of 2
ENSG00000294970	ENST00000727121.1	n.202-7586A>G		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.781 AC: 118808 AN: 152060 Hom.: 46493 Cov.: 33

Gnomad AFR AF: 0.801

Gnomad AMI AF: 0.715

Gnomad AMR AF: 0.800

Gnomad ASJ AF: 0.756

Gnomad EAS AF: 0.886

Gnomad SAS AF: 0.814

Gnomad FIN AF: 0.765

Gnomad MID AF: 0.696

Gnomad NFE AF: 0.761

Gnomad OTH AF: 0.761

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

GnomAD4 genome AF: 0.781 AC: 118912 AN: 152178 Hom.: 46540 Cov.: 33 AF XY: 0.784 AC XY: 58353 AN XY: 74406

African (AFR) AF: 0.801 AC: 33285 AN: 41544

American (AMR) AF: 0.800 AC: 12219 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.756 AC: 2625 AN: 3472

East Asian (EAS) AF: 0.886 AC: 4586 AN: 5176

South Asian (SAS) AF: 0.813 AC: 3920 AN: 4822

European-Finnish (FIN) AF: 0.765 AC: 8110 AN: 10604

Middle Eastern (MID) AF: 0.701 AC: 206 AN: 294

European-Non Finnish (NFE) AF: 0.761 AC: 51700 AN: 67972

Other (OTH) AF: 0.762 AC: 1610 AN: 2114

Alfa AF: 0.772 Hom.: 24867

Bravo AF: 0.787

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.97
DANN	Benign	0.61
PhyloP100		-0.30

Splicing

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

Other links and lift over

dbSNP: rs7185124; hg19: chr16-13750694;