rs506960

Variant names:

• chr8-8772759-A-C
• rs506960
• ENST00000519147.1:n.134+8543T>G

Variant summary

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

The ENST00000522213.5(ENSG00000254367):​n.374+9347T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.353 in 151,916 control chromosomes in the GnomAD database, including 10,411 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 0.35 (10411 hom., cov: 31)
• Consequence: ENSG00000254367 ENST00000522213.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.713
• Publications: 3 publications found

Genes affected

ENSG00000254367 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.488 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000522213.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000254367	ENST00000519147.1	TSL:3	n.134+8543T>G		intron	N/A
	ENSG00000254367	ENST00000522213.5	TSL:2	n.374+9347T>G		intron	N/A
	ENSG00000254367	ENST00000765578.1		n.314+6923T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.353 AC: 53578 AN: 151798 Hom.: 10394 Cov.: 31

Gnomad AFR AF: 0.493

Gnomad AMI AF: 0.209

Gnomad AMR AF: 0.228

Gnomad ASJ AF: 0.309

Gnomad EAS AF: 0.142

Gnomad SAS AF: 0.216

Gnomad FIN AF: 0.321

Gnomad MID AF: 0.392

Gnomad NFE AF: 0.330

Gnomad OTH AF: 0.352

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

GnomAD4 genome AF: 0.353 AC: 53634 AN: 151916 Hom.: 10411 Cov.: 31 AF XY: 0.346 AC XY: 25682 AN XY: 74252

African (AFR) AF: 0.494 AC: 20441 AN: 41408

American (AMR) AF: 0.228 AC: 3475 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.309 AC: 1072 AN: 3464

East Asian (EAS) AF: 0.142 AC: 735 AN: 5172

South Asian (SAS) AF: 0.216 AC: 1039 AN: 4808

European-Finnish (FIN) AF: 0.321 AC: 3380 AN: 10544

Middle Eastern (MID) AF: 0.397 AC: 116 AN: 292

European-Non Finnish (NFE) AF: 0.330 AC: 22451 AN: 67960

Other (OTH) AF: 0.349 AC: 734 AN: 2106

Alfa AF: 0.344 Hom.: 2934

Bravo AF: 0.350

Asia WGS AF: 0.199 AC: 695 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	2.8
DANN	Benign	0.72
PhyloP100		-0.71

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs506960;

hg19: chr8-8630269;