22-18937443-G-T

Variant names:

• chr22-18937443-G-T
• rs9604911
• ENST00000638240.1:c.514-2230G>T

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The ENST00000638240.1(ENSG00000283809):​c.514-2230G>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 0.43 (973 hom., cov: 3)
  • Failed GnomAD Quality Control
• Consequence: ENSG00000283809 ENST00000638240.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.312
• Publications: 13 publications found

Genes affected

ENSG00000283809 (HGNC:):

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000638240.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LOC122455341	NR_173080.2		n.318G>T		non_coding_transcript_exon	Exon 2 of 4

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000283809	ENST00000638240.1	TSL:5	c.514-2230G>T		intron	N/A	ENSP00000492446.1
	ENSG00000284294	ENST00000640084.1	TSL:5	n.330G>T		non_coding_transcript_exon	Exon 2 of 4

Frequencies

GnomAD3 genomes AF: 0.430 AC: 3951 AN: 9178 Hom.: 974 Cov.: 3

Gnomad AFR AF: 0.392

Gnomad AMI AF: 0.268

Gnomad AMR AF: 0.472

Gnomad ASJ AF: 0.500

Gnomad EAS AF: 0.638

Gnomad SAS AF: 0.346

Gnomad FIN AF: 0.516

Gnomad MID AF: 0.333

Gnomad NFE AF: 0.400

Gnomad OTH AF: 0.438

GnomAD4 exome Data not reliable, filtered out with message: AC0;AS_VQSR AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.430 AC: 3948 AN: 9190 Hom.: 973 Cov.: 3 AF XY: 0.443 AC XY: 1850 AN XY: 4172

African (AFR) AF: 0.392 AC: 1138 AN: 2906

American (AMR) AF: 0.471 AC: 461 AN: 978

Ashkenazi Jewish (ASJ) AF: 0.500 AC: 102 AN: 204

East Asian (EAS) AF: 0.642 AC: 430 AN: 670

South Asian (SAS) AF: 0.350 AC: 89 AN: 254

European-Finnish (FIN) AF: 0.516 AC: 296 AN: 574

Middle Eastern (MID) AF: 0.333 AC: 12 AN: 36

European-Non Finnish (NFE) AF: 0.400 AC: 1350 AN: 3376

Other (OTH) AF: 0.404 AC: 55 AN: 136

Alfa AF: 0.245 Hom.: 12314

Asia WGS AF: 0.407 AC: 1412 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.3
DANN	Benign	0.54
PhyloP100		0.31

Splicing

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

Other links and lift over

dbSNP: rs9604911; hg19: chr22-18924956;