rs12667374

chr7-69236985-G-A

Variant summary

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

The ENST00000435148.1(ENSG00000225718):n.591-12178C>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 0.0311 in 152,294 control chromosomes in the GnomAD database, including 109 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 0.031 (109 hom., cov: 32)
• Consequence: ENST00000435148.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.449

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0565 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000435148.1	n.591-12178C>T		intron_variant, non_coding_transcript_variant		3
	ENST00000670444.1	n.530+34980C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0311 AC: 4736 AN: 152176 Hom.: 110 Cov.: 32

Gnomad AFR AF: 0.00960

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0315

Gnomad ASJ AF: 0.00922

Gnomad EAS AF: 0.0618

Gnomad SAS AF: 0.00892

Gnomad FIN AF: 0.0208

Gnomad MID AF: 0.00949

Gnomad NFE AF: 0.0467

Gnomad OTH AF: 0.0296

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

GnomAD4 genome AF: 0.0311 AC: 4733 AN: 152294 Hom.: 109 Cov.: 32 AF XY: 0.0292 AC XY: 2177 AN XY: 74466

Gnomad4 AFR AF: 0.00957

Gnomad4 AMR AF: 0.0314

Gnomad4 ASJ AF: 0.00922

Gnomad4 EAS AF: 0.0621

Gnomad4 SAS AF: 0.00851

Gnomad4 FIN AF: 0.0208

Gnomad4 NFE AF: 0.0466

Gnomad4 OTH AF: 0.0298

Alfa AF: 0.0416 Hom.: 89

Bravo AF: 0.0325

Asia WGS AF: 0.0370 AC: 128 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	7.3
Dann	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12667374; hg19: chr7-68701972;