rs7149097

Variant names:

• chr14-103073332-A-G
• rs7149097
• ENST00000755126.1:n.-152T>C

Your query was ambiguous. Multiple possible variants found:

• chr14-103073332-A-G
• chr14-103073332-A-T

Variant summary

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

The ENST00000755126.1(ENSG00000298368):​n.-152T>C variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.85 in 152,194 control chromosomes in the GnomAD database, including 55,456 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 0.85 (55456 hom., cov: 33)
• Consequence: ENSG00000298368 ENST00000755126.1 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.658
• Publications: 7 publications found

Genes affected

ENSG00000298368 (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 (AFR) allele frequency at 95% confidence interval = 0.948 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000755126.1. 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
	ENSG00000298368	ENST00000755126.1		n.-152T>C		upstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.850 AC: 129221 AN: 152076 Hom.: 55391 Cov.: 33

Gnomad AFR AF: 0.956

Gnomad AMI AF: 0.814

Gnomad AMR AF: 0.782

Gnomad ASJ AF: 0.877

Gnomad EAS AF: 0.651

Gnomad SAS AF: 0.757

Gnomad FIN AF: 0.786

Gnomad MID AF: 0.851

Gnomad NFE AF: 0.831

Gnomad OTH AF: 0.857

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

GnomAD4 genome AF: 0.850 AC: 129342 AN: 152194 Hom.: 55456 Cov.: 33 AF XY: 0.842 AC XY: 62623 AN XY: 74398

African (AFR) AF: 0.956 AC: 39705 AN: 41546

American (AMR) AF: 0.782 AC: 11960 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.877 AC: 3045 AN: 3472

East Asian (EAS) AF: 0.652 AC: 3356 AN: 5148

South Asian (SAS) AF: 0.756 AC: 3656 AN: 4834

European-Finnish (FIN) AF: 0.786 AC: 8333 AN: 10602

Middle Eastern (MID) AF: 0.871 AC: 256 AN: 294

European-Non Finnish (NFE) AF: 0.831 AC: 56480 AN: 67978

Other (OTH) AF: 0.857 AC: 1810 AN: 2112

Alfa AF: 0.833 Hom.: 214099

Bravo AF: 0.854

Asia WGS AF: 0.779 AC: 2708 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	0.32
DANN	Benign	0.38
PhyloP100		-0.66

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: rs7149097;

hg19: chr14-103539669;