rs12159761

Variant names:

• chr22-38876636-C-G
• rs12159761
• ENST00000717626.1:n.231+4706C>G

Variant summary

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

The ENST00000717626.1(ENSG00000288106):​n.231+4706C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.198 in 152,018 control chromosomes in the GnomAD database, including 9,475 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 0.20 (9475 hom., cov: 31)
• Consequence: ENSG00000288106 ENST00000717626.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.607
• Publications: 4 publications found

Genes affected

ENSG00000288106 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.662 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
ENSG00000288106	ENST00000717626.1	n.231+4706C>G		intron_variant	Intron 1 of 4
ENSG00000288106	ENST00000717627.1	n.61+4706C>G		intron_variant	Intron 1 of 4
ENSG00000288106	ENST00000793132.1	n.53+4706C>G		intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes AF: 0.197 AC: 29976 AN: 151900 Hom.: 9432 Cov.: 31

Gnomad AFR AF: 0.668

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.0775

Gnomad ASJ AF: 0.00952

Gnomad EAS AF: 0.000385

Gnomad SAS AF: 0.00728

Gnomad FIN AF: 0.00151

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.0120

Gnomad OTH AF: 0.137

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

GnomAD4 genome AF: 0.198 AC: 30077 AN: 152018 Hom.: 9475 Cov.: 31 AF XY: 0.191 AC XY: 14172 AN XY: 74302

African (AFR) AF: 0.668 AC: 27678 AN: 41410

American (AMR) AF: 0.0774 AC: 1183 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.00952 AC: 33 AN: 3468

East Asian (EAS) AF: 0.000386 AC: 2 AN: 5180

South Asian (SAS) AF: 0.00666 AC: 32 AN: 4802

European-Finnish (FIN) AF: 0.00151 AC: 16 AN: 10572

Middle Eastern (MID) AF: 0.0952 AC: 28 AN: 294

European-Non Finnish (NFE) AF: 0.0120 AC: 816 AN: 67988

Other (OTH) AF: 0.136 AC: 288 AN: 2114

Alfa AF: 0.121 Hom.: 689

Bravo AF: 0.225

Asia WGS AF: 0.0540 AC: 188 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.1
DANN	Benign	0.55
PhyloP100		-0.61

Splicing

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

Other links and lift over

dbSNP: rs12159761; hg19: chr22-39272641;