rs562106

Variant names:

• chr6-95971274-A-C
• rs562106
• ENST00000658251.2:n.168+43653T>G

Your query was ambiguous. Multiple possible variants found:

• chr6-95971274-A-C
• chr6-95971274-A-G
• chr6-95971274-A-T

Variant summary

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

The ENST00000658251.2(ENSG00000287578):​n.168+43653T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.141 in 151,558 control chromosomes in the GnomAD database, including 1,722 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 0.14 (1722 hom., cov: 30)
• Consequence: ENSG00000287578 ENST00000658251.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.108
• Publications: 1 publications found

Genes affected

ENSG00000287578 (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 (AMR) allele frequency at 95% confidence interval = 0.192 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000658251.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000287578	ENST00000658251.2		n.168+43653T>G		intron	N/A
	ENSG00000287578	ENST00000668456.1		n.105+44013T>G		intron	N/A
	ENSG00000287578	ENST00000780318.1		n.112+44013T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.141 AC: 21359 AN: 151446 Hom.: 1718 Cov.: 30

Gnomad AFR AF: 0.165

Gnomad AMI AF: 0.159

Gnomad AMR AF: 0.197

Gnomad ASJ AF: 0.166

Gnomad EAS AF: 0.00545

Gnomad SAS AF: 0.165

Gnomad FIN AF: 0.0674

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.133

Gnomad OTH AF: 0.125

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

GnomAD4 genome AF: 0.141 AC: 21388 AN: 151558 Hom.: 1722 Cov.: 30 AF XY: 0.140 AC XY: 10388 AN XY: 74082

African (AFR) AF: 0.166 AC: 6843 AN: 41318

American (AMR) AF: 0.198 AC: 2997 AN: 15168

Ashkenazi Jewish (ASJ) AF: 0.166 AC: 575 AN: 3464

East Asian (EAS) AF: 0.00546 AC: 28 AN: 5130

South Asian (SAS) AF: 0.164 AC: 790 AN: 4804

European-Finnish (FIN) AF: 0.0674 AC: 713 AN: 10574

Middle Eastern (MID) AF: 0.0986 AC: 29 AN: 294

European-Non Finnish (NFE) AF: 0.133 AC: 9011 AN: 67796

Other (OTH) AF: 0.122 AC: 257 AN: 2100

Alfa AF: 0.0536 Hom.: 61

Bravo AF: 0.149

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.62
DANN	Benign	0.38
PhyloP100		0.11

Splicing

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

Other links and lift over

dbSNP: rs562106; hg19: chr6-96419150;