rs9498419

Variant names:

• chr6-100889735-A-C
• rs9498419
• ENST00000604292.1:n.133A>C

Your query was ambiguous. Multiple possible variants found:

• chr6-100889735-A-C
• chr6-100889735-A-G

Variant summary

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

The ENST00000604292.1(ENSG00000270987):​n.133A>C 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)
• Consequence: ENSG00000270987 ENST00000604292.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.89
• Publications: 6 publications found

Genes affected

ENSG00000270987 (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=-0.74).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC728098		n.100889735A>C		intragenic_variant
LOC107984041	XR_002956381.2	n.199-2263A>C		intron_variant	Intron 1 of 6
LOC107984041	XR_002956382.2	n.199-2263A>C		intron_variant	Intron 1 of 3
LOC107984041	XR_007059692.1	n.199-2263A>C		intron_variant	Intron 1 of 7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000270987	ENST00000604292.1	n.133A>C		non_coding_transcript_exon_variant	Exon 1 of 1	6
ENSG00000260000	ENST00000801152.1	n.522A>C		non_coding_transcript_exon_variant	Exon 2 of 2
ENSG00000260000	ENST00000801153.1	n.527A>C		non_coding_transcript_exon_variant	Exon 2 of 2
ENSG00000260000	ENST00000801154.1	n.528A>C		non_coding_transcript_exon_variant	Exon 2 of 2

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 47

GnomAD4 genome Cov.: 33

Alfa AF: 0.00 Hom.: 3206

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	9.3
DANN	Benign	0.75
PhyloP100		1.9

Splicing

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

Other links and lift over

dbSNP: rs9498419; hg19: chr6-101337611;