rs575959

Variant names:

• chr22-23947178-T-A
• rs575959
• ENST00000703580.1:n.310-20658A>T

Your query was ambiguous. Multiple possible variants found:

• chr22-23947178-T-A
• chr22-23947178-T-C
• chr22-23947178-T-G

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BP4_Strong BS2

The ENST00000703580.1(ENSG00000290199):​n.310-20658A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.34 (5942 hom., cov: 17)
• Consequence: ENSG00000290199 ENST00000703580.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.05
• Publications: 7 publications found

Genes affected

ENSG00000290199 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -8 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BS2: High Homozygotes in GnomAd4 at 5942 gene

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
ENSG00000290199	ENST00000703580.1	n.310-20658A>T		intron_variant	Intron 2 of 3
ENSG00000290199	ENST00000717616.1	n.136-20658A>T		intron_variant	Intron 1 of 2
ENSG00000290199	ENST00000717617.1	n.136-20658A>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.343 AC: 28492 AN: 83066 Hom.: 5935 Cov.: 17

Gnomad AFR AF: 0.271

Gnomad AMI AF: 0.491

Gnomad AMR AF: 0.350

Gnomad ASJ AF: 0.327

Gnomad EAS AF: 0.149

Gnomad SAS AF: 0.360

Gnomad FIN AF: 0.354

Gnomad MID AF: 0.464

Gnomad NFE AF: 0.396

Gnomad OTH AF: 0.341

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

GnomAD4 genome AF: 0.343 AC: 28514 AN: 83132 Hom.: 5942 Cov.: 17 AF XY: 0.338 AC XY: 13458 AN XY: 39782

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.

African (AFR) AF: 0.272 AC: 6241 AN: 22974

American (AMR) AF: 0.350 AC: 2720 AN: 7762

Ashkenazi Jewish (ASJ) AF: 0.327 AC: 661 AN: 2022

East Asian (EAS) AF: 0.148 AC: 471 AN: 3172

South Asian (SAS) AF: 0.361 AC: 733 AN: 2030

European-Finnish (FIN) AF: 0.354 AC: 1711 AN: 4832

Middle Eastern (MID) AF: 0.461 AC: 82 AN: 178

European-Non Finnish (NFE) AF: 0.396 AC: 15300 AN: 38604

Other (OTH) AF: 0.338 AC: 377 AN: 1114

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5. (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

Alfa AF: 0.00 Hom.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.65
DANN	Benign	0.058
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs575959; hg19: chr22-24289365;