rs9600764

Variant names:

• chr13-76736658-A-G
• rs9600764
• ENST00000648060.1:n.230-7148T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000648060.1(ENSG00000285572):​n.230-7148T>C variant causes a intron 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: ENSG00000285572 ENST00000648060.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.852
• Publications: 3 publications found

Genes affected

ENSG00000285572 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
LOC105370265	XR_001749923.2	n.118-7148T>C		intron_variant	Intron 1 of 3
LOC105370265	XR_001749924.2	n.2406+5782T>C		intron_variant	Intron 1 of 3
LOC105370265	XR_001749925.2	n.338-7148T>C		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000285572	ENST00000648060.1	n.230-7148T>C		intron_variant	Intron 2 of 4
ENSG00000285572	ENST00000791170.1	n.178-7148T>C		intron_variant	Intron 2 of 2
ENSG00000285572	ENST00000791172.1	n.311-7148T>C		intron_variant	Intron 1 of 3

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

African (AFR) AF: 0.163 AC: 6754 AN: 41518

American (AMR) AF: 0.0450 AC: 688 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0619 AC: 215 AN: 3472

East Asian (EAS) AF: 0.00309 AC: 16 AN: 5182

South Asian (SAS) AF: 0.0116 AC: 56 AN: 4828

European-Finnish (FIN) AF: 0.00669 AC: 71 AN: 10614

Middle Eastern (MID) AF: 0.0850 AC: 25 AN: 294

European-Non Finnish (NFE) AF: 0.0353 AC: 2398 AN: 68008

Other (OTH) AF: 0.0598 AC: 126 AN: 2106

Alfa AF: 0.0464 Hom.: 401

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
PhyloP100		-0.85

Splicing

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

Other links and lift over

dbSNP: rs9600764; hg19: chr13-77310793;