rs12700594

Positions:

• chr7-3117067-G-A
• chr7-3117067-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000667422.1(ENSG00000228334):​n.75+908C>T variant causes a intron, non coding transcript 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: ENST00000667422.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.787

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
LOC105375130	XR_007060191.1	n.60+908C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000667422.1	n.75+908C>T		intron_variant, non_coding_transcript_variant
	ENST00000703009.1	n.60+908C>T		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.507

Gnomad4 AMR AF: 0.524

Gnomad4 ASJ AF: 0.641

Gnomad4 EAS AF: 0.387

Gnomad4 SAS AF: 0.551

Gnomad4 FIN AF: 0.510

Gnomad4 NFE AF: 0.552

Gnomad4 OTH AF: 0.562

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12700594; hg19: chr7-3156701;