rs9604911

Positions:

• chr22-18937443-G-T

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong

The NR_173080.1(LOC122455341):​n.69G>T variant causes a non coding transcript exon 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: LOC122455341 NR_173080.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.312

Genes affected

(HGNC:):

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

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

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC122455341	NR_173080.1	n.69G>T		non_coding_transcript_exon_variant	1/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000640084.1	n.330G>T		non_coding_transcript_exon_variant	2/4	5

Frequencies

GnomAD3 genomes AF: 0.00 AC: 3951 AN: 9178 Hom.: 974 Cov.: 3 FAILED QC

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

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

Gnomad4 AFR AF: 0.392

Gnomad4 AMR AF: 0.471

Gnomad4 ASJ AF: 0.500

Gnomad4 EAS AF: 0.642

Gnomad4 SAS AF: 0.350

Gnomad4 FIN AF: 0.516

Gnomad4 NFE AF: 0.400

Gnomad4 OTH AF: 0.404

Alfa AF: 0.242 Hom.: 7340

Asia WGS AF: 0.407 AC: 1412 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	1.3
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9604911; hg19: chr22-18924956;