rs12700667

Variant names:

• chr7-25862019-G-A
• rs12700667
• ENST00000666265.2:n.221+125C>T

Variant summary

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

The ENST00000666265.2(ENSG00000286725):​n.221+125C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.623 in 152,008 control chromosomes in the GnomAD database, including 31,319 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 (31319 hom., cov: 32)
• Consequence: ENSG00000286725 ENST00000666265.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.274
• Publications: 69 publications found

Genes affected

ENSG00000286725 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.66).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.734 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000666265.2. 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
	ENSG00000286725	ENST00000666265.2		n.221+125C>T		intron	N/A
	ENSG00000286725	ENST00000812174.1		n.200+125C>T		intron	N/A
	ENSG00000286725	ENST00000812175.1		n.183+125C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.624 AC: 94720 AN: 151890 Hom.: 31324 Cov.: 32

Gnomad AFR AF: 0.444

Gnomad AMI AF: 0.803

Gnomad AMR AF: 0.675

Gnomad ASJ AF: 0.779

Gnomad EAS AF: 0.183

Gnomad SAS AF: 0.488

Gnomad FIN AF: 0.711

Gnomad MID AF: 0.655

Gnomad NFE AF: 0.740

Gnomad OTH AF: 0.652

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

GnomAD4 genome AF: 0.623 AC: 94744 AN: 152008 Hom.: 31319 Cov.: 32 AF XY: 0.619 AC XY: 45988 AN XY: 74294

African (AFR) AF: 0.444 AC: 18374 AN: 41428

American (AMR) AF: 0.674 AC: 10306 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.779 AC: 2703 AN: 3470

East Asian (EAS) AF: 0.182 AC: 943 AN: 5174

South Asian (SAS) AF: 0.486 AC: 2340 AN: 4812

European-Finnish (FIN) AF: 0.711 AC: 7512 AN: 10560

Middle Eastern (MID) AF: 0.656 AC: 193 AN: 294

European-Non Finnish (NFE) AF: 0.740 AC: 50273 AN: 67962

Other (OTH) AF: 0.648 AC: 1368 AN: 2112

Alfa AF: 0.691 Hom.: 108615

Bravo AF: 0.611

Asia WGS AF: 0.402 AC: 1403 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.66
CADD	Benign	15
DANN	Benign	0.72
PhyloP100		0.27

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: rs12700667;

hg19: chr7-25901639;