rs6472155

Variant names:

• chr8-64817650-G-A
• rs6472155
• ENST00000833569.1:n.685G>A

Your query was ambiguous. Multiple possible variants found:

• chr8-64817650-G-A
• chr8-64817650-G-C
• chr8-64817650-G-T

Variant summary

Our verdict is Likely benign. The variant received -6 ACMG points: 2P and 8B. PVS1_Moderate BA1

The ENST00000833568.1(ENSG00000287998):​n.664+1G>A variant causes a splice donor, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.533 in 151,880 control chromosomes in the GnomAD database, including 21,774 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 0.53 (21773 hom., cov: 31)
  • Exomes 𝑓: 0.38 (1 hom.)
• Consequence: ENSG00000287998 ENST00000833568.1 splice_donor, intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0400
• Publications: 14 publications found

Genes affected

ENSG00000287998 (HGNC:):

ACMG classification

Our verdict: Likely_benign. The variant received -6 ACMG points.

• PVS1: Splicing +-2 bp (donor or acceptor) variant, product NOT destroyed by NMD, known LOF gene. Cryptic splice site detected, with MaxEntScore 8.2, offset of -48, new splice context is: gtgGTaaga. Cryptic site results in inframe change. If cryptic site found is not functional and variant results in exon loss, it results in inframe change.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.689 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000833568.1. 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
	LOC105375878	NR_188109.1		n.-47C>T		upstream_gene	N/A
	LOC105375878	NR_188110.1		n.-47C>T		upstream_gene	N/A
	LOC105375878	NR_188111.1		n.-47C>T		upstream_gene	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000287998	ENST00000833569.1		n.685G>A		non_coding_transcript_exon	Exon 3 of 3
	ENSG00000287998	ENST00000665380.1		n.367+13739G>A		intron	N/A
	ENSG00000287998	ENST00000833561.1		n.356+13739G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.533 AC: 80823 AN: 151754 Hom.: 21743 Cov.: 31

Gnomad AFR AF: 0.544

Gnomad AMI AF: 0.337

Gnomad AMR AF: 0.565

Gnomad ASJ AF: 0.545

Gnomad EAS AF: 0.708

Gnomad SAS AF: 0.600

Gnomad FIN AF: 0.492

Gnomad MID AF: 0.484

Gnomad NFE AF: 0.509

Gnomad OTH AF: 0.516

GnomAD4 exome AF: 0.375 AC: 3 AN: 8 Hom.: 1 AF XY: 0.375 AC XY: 3 AN XY: 8

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AF: 1.00 AC: 2 AN: 2

East Asian (EAS) AF: 0.500 AC: 1 AN: 2

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 4

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.533 AC: 80892 AN: 151872 Hom.: 21773 Cov.: 31 AF XY: 0.534 AC XY: 39604 AN XY: 74192

African (AFR) AF: 0.544 AC: 22495 AN: 41384

American (AMR) AF: 0.565 AC: 8632 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.545 AC: 1890 AN: 3468

East Asian (EAS) AF: 0.708 AC: 3650 AN: 5154

South Asian (SAS) AF: 0.601 AC: 2893 AN: 4816

European-Finnish (FIN) AF: 0.492 AC: 5158 AN: 10494

Middle Eastern (MID) AF: 0.476 AC: 140 AN: 294

European-Non Finnish (NFE) AF: 0.510 AC: 34631 AN: 67970

Other (OTH) AF: 0.520 AC: 1096 AN: 2106

Alfa AF: 0.519 Hom.: 55196

Bravo AF: 0.537

Asia WGS AF: 0.666 AC: 2312 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	3.4
DANN	Benign	0.64
PhyloP100		0.040

Splicing

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

Other links and lift over

dbSNP: rs6472155; hg19: chr8-65730207;