rs12154270

Variant names:

• chr7-84714942-C-T
• rs12154270
• ENST00000775795.1:n.73+5613G>A

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000775795.1(ENSG00000301054):​n.73+5613G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.148 in 152,008 control chromosomes in the GnomAD database, including 2,013 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 0.15 (2013 hom., cov: 31)
• Consequence: ENSG00000301054 ENST00000775795.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.670
• Publications: 3 publications found

Genes affected

ENSG00000301054 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.36).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.211 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
ENSG00000301054	ENST00000775795.1	n.73+5613G>A		intron_variant	Intron 1 of 2
ENSG00000301054	ENST00000775796.1	n.46+5613G>A		intron_variant	Intron 1 of 3
ENSG00000301054	ENST00000775800.1	n.96+5613G>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.148 AC: 22496 AN: 151890 Hom.: 2015 Cov.: 31

Gnomad AFR AF: 0.0564

Gnomad AMI AF: 0.198

Gnomad AMR AF: 0.128

Gnomad ASJ AF: 0.178

Gnomad EAS AF: 0.0672

Gnomad SAS AF: 0.126

Gnomad FIN AF: 0.145

Gnomad MID AF: 0.199

Gnomad NFE AF: 0.214

Gnomad OTH AF: 0.164

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

GnomAD4 genome AF: 0.148 AC: 22494 AN: 152008 Hom.: 2013 Cov.: 31 AF XY: 0.146 AC XY: 10820 AN XY: 74282

African (AFR) AF: 0.0564 AC: 2339 AN: 41496

American (AMR) AF: 0.128 AC: 1948 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.178 AC: 619 AN: 3468

East Asian (EAS) AF: 0.0673 AC: 347 AN: 5154

South Asian (SAS) AF: 0.126 AC: 609 AN: 4816

European-Finnish (FIN) AF: 0.145 AC: 1531 AN: 10570

Middle Eastern (MID) AF: 0.201 AC: 59 AN: 294

European-Non Finnish (NFE) AF: 0.214 AC: 14519 AN: 67946

Other (OTH) AF: 0.162 AC: 342 AN: 2106

Alfa AF: 0.194 Hom.: 5024

Bravo AF: 0.140

Asia WGS AF: 0.0950 AC: 330 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.36
CADD	Benign	17
DANN	Benign	0.79
PhyloP100		0.67

Splicing

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

Other links and lift over

dbSNP: rs12154270; hg19: chr7-84344258;