rs1454535

Variant names:

• chr2-220365201-A-C
• rs1454535
• ENST00000432993.1:n.427+42980A>C

Your query was ambiguous. Multiple possible variants found:

• chr2-220365201-A-C
• chr2-220365201-A-G
• chr2-220365201-A-T

Variant summary

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

The ENST00000432993.1(ENSG00000288902):​n.427+42980A>C variant causes a intron 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: 32)
• Consequence: ENSG00000288902 ENST00000432993.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0500
• Publications: 6 publications found

Genes affected

ENSG00000288902 (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=-0.84).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105373893	XR_001739889.2	n.394+42980A>C		intron_variant	Intron 3 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000288902	ENST00000432993.1	n.427+42980A>C		intron_variant	Intron 2 of 3	3
ENSG00000288902	ENST00000830324.1	n.768+43026A>C		intron_variant	Intron 5 of 5
ENSG00000288902	ENST00000830325.1	n.442+39967A>C		intron_variant	Intron 4 of 5

Frequencies

GnomAD3 genomes Cov.: 32

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

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	7.0
DANN	Benign	0.76
PhyloP100		-0.050

Splicing

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

Other links and lift over

dbSNP: rs1454535; hg19: chr2-221229922;