rs10484507

Variant names:

• chr6-164185287-A-G
• rs10484507
• ENST00000850151.1:n.312-52467A>G

Variant summary

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

The ENST00000850151.1(ENSG00000288696):​n.312-52467A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0796 in 152,266 control chromosomes in the GnomAD database, including 589 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 0.080 (589 hom., cov: 33)
• Consequence: ENSG00000288696 ENST00000850151.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.459
• Publications: 2 publications found

Genes affected

ENSG00000288696 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.117 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
ENSG00000288696	ENST00000850151.1	n.312-52467A>G		intron_variant	Intron 3 of 4
ENSG00000288696	ENST00000850152.1	n.372-52467A>G		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.0796 AC: 12117 AN: 152148 Hom.: 590 Cov.: 33

Gnomad AFR AF: 0.120

Gnomad AMI AF: 0.148

Gnomad AMR AF: 0.0488

Gnomad ASJ AF: 0.0234

Gnomad EAS AF: 0.000578

Gnomad SAS AF: 0.0743

Gnomad FIN AF: 0.0521

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.0754

Gnomad OTH AF: 0.0664

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

GnomAD4 genome AF: 0.0796 AC: 12117 AN: 152266 Hom.: 589 Cov.: 33 AF XY: 0.0768 AC XY: 5721 AN XY: 74448

African (AFR) AF: 0.120 AC: 4967 AN: 41538

American (AMR) AF: 0.0487 AC: 746 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.0234 AC: 81 AN: 3468

East Asian (EAS) AF: 0.000579 AC: 3 AN: 5182

South Asian (SAS) AF: 0.0735 AC: 355 AN: 4830

European-Finnish (FIN) AF: 0.0521 AC: 553 AN: 10608

Middle Eastern (MID) AF: 0.0340 AC: 10 AN: 294

European-Non Finnish (NFE) AF: 0.0754 AC: 5128 AN: 68012

Other (OTH) AF: 0.0657 AC: 139 AN: 2116

Alfa AF: 0.0773 Hom.: 521

Bravo AF: 0.0804

Asia WGS AF: 0.0470 AC: 166 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	1.4
DANN	Benign	0.75
PhyloP100		0.46

Splicing

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

Other links and lift over

dbSNP: rs10484507; hg19: chr6-164606319;