rs9600764

Positions:

• chr13-76736658-A-G

Variant summary

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

The ENST00000648060.1(ENSG00000285572):​n.230-7148T>C 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 0.068 in 152,232 control chromosomes in the GnomAD database, including 610 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 0.068 (610 hom., cov: 32)
• Consequence: ENST00000648060.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.852

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 = 0.159 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105370265	XR_001749923.2	n.118-7148T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000648060.1	n.230-7148T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0679 AC: 10322 AN: 152114 Hom.: 607 Cov.: 32

Gnomad AFR AF: 0.162

Gnomad AMI AF: 0.00548

Gnomad AMR AF: 0.0450

Gnomad ASJ AF: 0.0619

Gnomad EAS AF: 0.00308

Gnomad SAS AF: 0.0116

Gnomad FIN AF: 0.00669

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.0353

Gnomad OTH AF: 0.0590

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

GnomAD4 genome AF: 0.0680 AC: 10354 AN: 152232 Hom.: 610 Cov.: 32 AF XY: 0.0649 AC XY: 4828 AN XY: 74430

Gnomad4 AFR AF: 0.163

Gnomad4 AMR AF: 0.0450

Gnomad4 ASJ AF: 0.0619

Gnomad4 EAS AF: 0.00309

Gnomad4 SAS AF: 0.0116

Gnomad4 FIN AF: 0.00669

Gnomad4 NFE AF: 0.0353

Gnomad4 OTH AF: 0.0598

Alfa AF: 0.0430 Hom.: 257

Bravo AF: 0.0745

Asia WGS AF: 0.0330 AC: 116 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	0.37
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9600764; hg19: chr13-77310793;