rs6592945

chr7-51651833-T-Achr7-51651833-T-C

Variant summary

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

The ENST00000648455.1(ENSG00000285741):n.353-12875T>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 0.608 in 151,992 control chromosomes in the GnomAD database, including 28,570 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 0.61 (28570 hom., cov: 32)
• Consequence: ENST00000648455.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00100

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.706 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
	ENST00000648455.1	n.353-12875T>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.608 AC: 92284 AN: 151874 Hom.: 28535 Cov.: 32

Gnomad AFR AF: 0.713

Gnomad AMI AF: 0.455

Gnomad AMR AF: 0.673

Gnomad ASJ AF: 0.554

Gnomad EAS AF: 0.632

Gnomad SAS AF: 0.660

Gnomad FIN AF: 0.554

Gnomad MID AF: 0.630

Gnomad NFE AF: 0.536

Gnomad OTH AF: 0.630

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

GnomAD4 genome AF: 0.608 AC: 92374 AN: 151992 Hom.: 28570 Cov.: 32 AF XY: 0.613 AC XY: 45518 AN XY: 74284

Gnomad4 AFR AF: 0.713

Gnomad4 AMR AF: 0.673

Gnomad4 ASJ AF: 0.554

Gnomad4 EAS AF: 0.633

Gnomad4 SAS AF: 0.659

Gnomad4 FIN AF: 0.554

Gnomad4 NFE AF: 0.536

Gnomad4 OTH AF: 0.628

Alfa AF: 0.570 Hom.: 3070

Bravo AF: 0.621

Asia WGS AF: 0.641 AC: 2227 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	1.6
Dann	Benign	0.31

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6592945; hg19: chr7-51719529;