rs7987165

chr13-76570919-A-C

Variant summary

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

The ENST00000648060.1(ENSG00000285572):n.396-16100T>G 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 0.424 in 151,906 control chromosomes in the GnomAD database, including 13,941 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 (13941 hom., cov: 31)
• Consequence: ENST00000648060.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.108

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.586 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
	ENST00000648060.1	n.396-16100T>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.424 AC: 64427 AN: 151788 Hom.: 13928 Cov.: 31

Gnomad AFR AF: 0.433

Gnomad AMI AF: 0.256

Gnomad AMR AF: 0.333

Gnomad ASJ AF: 0.398

Gnomad EAS AF: 0.604

Gnomad SAS AF: 0.396

Gnomad FIN AF: 0.441

Gnomad MID AF: 0.399

Gnomad NFE AF: 0.430

Gnomad OTH AF: 0.415

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

GnomAD4 genome AF: 0.424 AC: 64473 AN: 151906 Hom.: 13941 Cov.: 31 AF XY: 0.425 AC XY: 31542 AN XY: 74272

Gnomad4 AFR AF: 0.433

Gnomad4 AMR AF: 0.332

Gnomad4 ASJ AF: 0.398

Gnomad4 EAS AF: 0.604

Gnomad4 SAS AF: 0.396

Gnomad4 FIN AF: 0.441

Gnomad4 NFE AF: 0.430

Gnomad4 OTH AF: 0.413

Alfa AF: 0.428 Hom.: 26081

Bravo AF: 0.415

Asia WGS AF: 0.455 AC: 1582 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
Cadd	Benign	5.7
Dann	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7987165; hg19: chr13-77145054;