rs2987460

Positions:

• chr1-234677730-A-G
• chr1-234677730-A-T

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The XR_949287.4(LOC105373208):​n.2065T>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: 32)
• Consequence: LOC105373208 XR_949287.4 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.123

Genes affected

LOC105373208 (HGNC:):

ACMG classification

Verdict is Likely_benign. Variant got -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105373208	XR_949287.4	n.2065T>C		non_coding_transcript_exon_variant	3/3
LOC105373209	XR_949289.3	n.75+1628A>G		intron_variant, non_coding_transcript_variant
LOC105373208	XR_007066951.1	n.3355T>C		non_coding_transcript_exon_variant	2/2
LOC105373209	XR_949288.3	n.166+1167A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000442382.1	n.97-4740T>C		intron_variant, non_coding_transcript_variant		2
	ENST00000664534.1	n.183-3081A>G		intron_variant, non_coding_transcript_variant
	ENST00000449012.1	n.110-3081A>G		intron_variant, non_coding_transcript_variant		3
	ENST00000453568.1	n.32-3081A>G		intron_variant, non_coding_transcript_variant		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	-0.90
CADD	Benign	3.3
DANN	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2987460; hg19: chr1-234813476;