rs12700594

Variant names:

• chr7-3117067-G-A
• rs12700594
• ENST00000667422.1:n.75+908C>T

Your query was ambiguous. Multiple possible variants found:

• chr7-3117067-G-A
• chr7-3117067-G-T

Variant summary

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

The ENST00000667422.1(ENSG00000217455):​n.75+908C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.531 in 152,022 control chromosomes in the GnomAD database, including 21,641 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 0.53 (21641 hom., cov: 32)
• Consequence: ENSG00000217455 ENST00000667422.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.787
• Publications: 2 publications found

Genes affected

ENSG00000217455 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.547 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105375130	XR_007060191.1	n.60+908C>T		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000217455	ENST00000667422.1	n.75+908C>T		intron_variant	Intron 1 of 1
ENSG00000217455	ENST00000703009.2	n.89+908C>T		intron_variant	Intron 1 of 1
ENSG00000217455	ENST00000716171.1	n.248+3656C>T		intron_variant	Intron 3 of 4

Frequencies

GnomAD3 genomes AF: 0.531 AC: 80720 AN: 151904 Hom.: 21636 Cov.: 32

Gnomad AFR AF: 0.507

Gnomad AMI AF: 0.649

Gnomad AMR AF: 0.524

Gnomad ASJ AF: 0.641

Gnomad EAS AF: 0.388

Gnomad SAS AF: 0.551

Gnomad FIN AF: 0.510

Gnomad MID AF: 0.614

Gnomad NFE AF: 0.552

Gnomad OTH AF: 0.569

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

GnomAD4 genome AF: 0.531 AC: 80762 AN: 152022 Hom.: 21641 Cov.: 32 AF XY: 0.529 AC XY: 39274 AN XY: 74290

African (AFR) AF: 0.507 AC: 21031 AN: 41470

American (AMR) AF: 0.524 AC: 8007 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.641 AC: 2226 AN: 3470

East Asian (EAS) AF: 0.387 AC: 2001 AN: 5164

South Asian (SAS) AF: 0.551 AC: 2653 AN: 4814

European-Finnish (FIN) AF: 0.510 AC: 5388 AN: 10574

Middle Eastern (MID) AF: 0.622 AC: 183 AN: 294

European-Non Finnish (NFE) AF: 0.552 AC: 37497 AN: 67950

Other (OTH) AF: 0.562 AC: 1185 AN: 2108

Alfa AF: 0.404 Hom.: 958

Bravo AF: 0.553

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	7.3
DANN	Benign	0.42
PhyloP100		0.79

Splicing

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

Other links and lift over

dbSNP: rs12700594; hg19: chr7-3156701;