rs2020930

chr17-30239023-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000577420.1(ENSG00000266120):n.60+223C>T variant causes a intron, non coding transcript 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: ENST00000577420.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.481

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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 male gnomad4 subpopulation. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd at 111 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105371720	XR_001752824.2	n.891+223C>T		intron_variant, non_coding_transcript_variant
LOC105371720	XR_007065695.1	n.755+223C>T		intron_variant, non_coding_transcript_variant
LOC105371720	XR_007065696.1	n.755+223C>T		intron_variant, non_coding_transcript_variant
LOC105371720	XR_007065698.1	n.755+223C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000577420.1	n.60+223C>T		intron_variant, non_coding_transcript_variant		3

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

Gnomad4 AFR AF: 0.0359

Gnomad4 AMR AF: 0.0316

Gnomad4 ASJ AF: 0.0744

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.0230

Gnomad4 FIN AF: 0.0238

Gnomad4 NFE AF: 0.0393

Gnomad4 OTH AF: 0.0416

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2020930; hg19: chr17-28566041;