chr9-121370602-A-T

Variant names:

• chr9-121370602-A-T
• rs1771889
• ENST00000637541.1:n.112A>T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000637541.1(ENSG00000227355):​n.112A>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 33)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: ENSG00000227355 ENST00000637541.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.424
• Publications: 8 publications found

Genes affected

ENSG00000227355 (HGNC:):

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000637541.1. 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
	LOC102723324	NR_187150.1		n.88A>T		non_coding_transcript_exon	Exon 1 of 3
	LOC102723324	NR_187151.1		n.88A>T		non_coding_transcript_exon	Exon 1 of 3
	LOC102723324	NR_187152.1		n.88A>T		non_coding_transcript_exon	Exon 1 of 3

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000227355	ENST00000637541.1	TSL:3	n.112A>T		non_coding_transcript_exon	Exon 1 of 3
	ENSG00000227355	ENST00000685727.2		n.159A>T		non_coding_transcript_exon	Exon 1 of 4
	ENSG00000227355	ENST00000688457.2		n.89A>T		non_coding_transcript_exon	Exon 1 of 4

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 36070 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 19186

African (AFR) AF: 0.00 AC: 0 AN: 1664

American (AMR) AF: 0.00 AC: 0 AN: 2352

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 1196

East Asian (EAS) AF: 0.00 AC: 0 AN: 2642

South Asian (SAS) AF: 0.00 AC: 0 AN: 3098

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 1484

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 158

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 21474

Other (OTH) AF: 0.00 AC: 0 AN: 2002

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	7.9
DANN	Benign	0.71
PhyloP100		0.42
PromoterAI		0.0067	Neutral

Splicing

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

Other links and lift over

dbSNP: rs1771889; hg19: chr9-124132880;