rs2020930

Variant names:

• chr17-30239023-C-T
• rs2020930
• ENST00000577420.2:n.259+223C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000577420.2(ENSG00000266120):​n.259+223C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0354 in 152,236 control chromosomes in the GnomAD database, including 111 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 0.035 (111 hom., cov: 31)
• Consequence: ENSG00000266120 ENST00000577420.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.481
• Publications: 3 publications found

Genes affected

ENSG00000266120 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BS1: Variant frequency is greater than expected in population nfe. GnomAd4 allele frequency = 0.0354 (5387/152236) while in subpopulation NFE AF = 0.0393 (2676/68010). AF 95% confidence interval is 0.0381. There are 111 homozygotes in GnomAd4. There are 2557 alleles in the male GnomAd4 subpopulation. Median coverage is 31. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 111 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105371720	XR_001752824.2	n.891+223C>T		intron_variant	Intron 3 of 3
LOC105371720	XR_007065695.1	n.755+223C>T		intron_variant	Intron 2 of 2
LOC105371720	XR_007065696.1	n.755+223C>T		intron_variant	Intron 2 of 2
LOC105371720	XR_007065698.1	n.755+223C>T		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000266120	ENST00000577420.2	n.259+223C>T		intron_variant	Intron 1 of 2	3
ENSG00000266120	ENST00000724730.1	n.257+223C>T		intron_variant	Intron 1 of 1
ENSG00000266120	ENST00000724731.1	n.720+223C>T		intron_variant	Intron 3 of 4
ENSG00000266120	ENST00000724732.1	n.170+223C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.0354 AC: 5385 AN: 152118 Hom.: 111 Cov.: 31

Gnomad AFR AF: 0.0359

Gnomad AMI AF: 0.00329

Gnomad AMR AF: 0.0317

Gnomad ASJ AF: 0.0744

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.0228

Gnomad FIN AF: 0.0238

Gnomad MID AF: 0.0796

Gnomad NFE AF: 0.0394

Gnomad OTH AF: 0.0420

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

GnomAD4 genome AF: 0.0354 AC: 5387 AN: 152236 Hom.: 111 Cov.: 31 AF XY: 0.0344 AC XY: 2557 AN XY: 74432

African (AFR) AF: 0.0359 AC: 1490 AN: 41524

American (AMR) AF: 0.0316 AC: 484 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.0744 AC: 258 AN: 3470

East Asian (EAS) AF: 0.00 AC: 0 AN: 5176

South Asian (SAS) AF: 0.0230 AC: 111 AN: 4826

European-Finnish (FIN) AF: 0.0238 AC: 253 AN: 10608

Middle Eastern (MID) AF: 0.0822 AC: 24 AN: 292

European-Non Finnish (NFE) AF: 0.0393 AC: 2676 AN: 68010

Other (OTH) AF: 0.0416 AC: 88 AN: 2116

Alfa AF: 0.0377 Hom.: 13

Bravo AF: 0.0354

Asia WGS AF: 0.0160 AC: 54 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.6
DANN	Benign	0.40
PhyloP100		-0.48

Splicing

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

Other links and lift over

dbSNP: rs2020930; hg19: chr17-28566041;