rs17023786

Variant names:

• chr1-119475362-G-C
• rs17023786
• ENST00000632456.2:n.768+8187C>G

Variant summary

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

The ENST00000632456.2(ENSG00000293080):​n.768+8187C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0515 in 152,208 control chromosomes in the GnomAD database, including 673 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 0.052 (673 hom., cov: 33)
• Consequence: ENSG00000293080 ENST00000632456.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.278
• Publications: 1 publications found

Genes affected

ENSG00000293080 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.173 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124904388	XR_007066503.1	n.570-436C>G		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000293080	ENST00000632456.2	n.768+8187C>G		intron_variant	Intron 6 of 6	6
ENSG00000293080	ENST00000756943.1	n.686-436C>G		intron_variant	Intron 5 of 5
ENSG00000293080	ENST00000756944.1	n.339+10089C>G		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.0513 AC: 7808 AN: 152090 Hom.: 667 Cov.: 33

Gnomad AFR AF: 0.176

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0215

Gnomad ASJ AF: 0.00230

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000830

Gnomad FIN AF: 0.000283

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.00137

Gnomad OTH AF: 0.0359

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

GnomAD4 genome AF: 0.0515 AC: 7841 AN: 152208 Hom.: 673 Cov.: 33 AF XY: 0.0495 AC XY: 3685 AN XY: 74436

African (AFR) AF: 0.177 AC: 7326 AN: 41498

American (AMR) AF: 0.0215 AC: 328 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.00230 AC: 8 AN: 3472

East Asian (EAS) AF: 0.00 AC: 0 AN: 5182

South Asian (SAS) AF: 0.000623 AC: 3 AN: 4818

European-Finnish (FIN) AF: 0.000283 AC: 3 AN: 10612

Middle Eastern (MID) AF: 0.0170 AC: 5 AN: 294

European-Non Finnish (NFE) AF: 0.00137 AC: 93 AN: 68028

Other (OTH) AF: 0.0355 AC: 75 AN: 2110

Alfa AF: 0.0426 Hom.: 52

Bravo AF: 0.0585

Asia WGS AF: 0.0130 AC: 46 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.3
DANN	Benign	0.44
PhyloP100		0.28

Splicing

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

Other links and lift over

dbSNP: rs17023786; hg19: chr1-120017985;