rs7973719

Positions:

• chr12-7182217-C-T

Variant summary

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

The ENST00000543061.1(ENSG00000255572):​n.324+6529G>A 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 0.425 in 151,972 control chromosomes in the GnomAD database, including 15,649 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 0.42 (15649 hom., cov: 31)
• Consequence: ENST00000543061.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.25

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.06).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.588 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000543061.1	n.324+6529G>A		intron_variant, non_coding_transcript_variant		2
	ENST00000545794.1	n.279+6529G>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.425 AC: 64516 AN: 151854 Hom.: 15639 Cov.: 31

Gnomad AFR AF: 0.188

Gnomad AMI AF: 0.632

Gnomad AMR AF: 0.598

Gnomad ASJ AF: 0.483

Gnomad EAS AF: 0.382

Gnomad SAS AF: 0.469

Gnomad FIN AF: 0.442

Gnomad MID AF: 0.497

Gnomad NFE AF: 0.521

Gnomad OTH AF: 0.468

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

GnomAD4 genome AF: 0.425 AC: 64528 AN: 151972 Hom.: 15649 Cov.: 31 AF XY: 0.425 AC XY: 31542 AN XY: 74254

Gnomad4 AFR AF: 0.187

Gnomad4 AMR AF: 0.598

Gnomad4 ASJ AF: 0.483

Gnomad4 EAS AF: 0.383

Gnomad4 SAS AF: 0.469

Gnomad4 FIN AF: 0.442

Gnomad4 NFE AF: 0.520

Gnomad4 OTH AF: 0.465

Alfa AF: 0.470 Hom.: 2198

Bravo AF: 0.427

Asia WGS AF: 0.413 AC: 1435 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.36
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7973719; hg19: chr12-7334813;