rs7987165

Variant names:

• chr13-76570919-A-C
• rs7987165
• ENST00000648060.1:n.396-16100T>G

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 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: ENSG00000285572 ENST00000648060.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.108

Genes affected

ENSG00000285572 (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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000285572	ENST00000648060.1	n.396-16100T>G		intron_variant	Intron 3 of 4

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;