rs10516439

Variant names:

• chr4-99382001-G-A
• rs10516439
• XR_001741777.2:n.2007C>T

Your query was ambiguous. Multiple possible variants found:

• chr4-99382001-G-A
• chr4-99382001-G-C
• chr4-99382001-G-T

Variant summary

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

The XR_001741777.2(LOC102723576):​n.2007C>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)
• Consequence: LOC102723576 XR_001741777.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.74
• Publications: 6 publications found

Genes affected

LOC102723576 (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=-0.93).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC102723576	XR_001741777.2	n.2007C>T		non_coding_transcript_exon_variant	Exon 4 of 4
LOC102723576	XR_427569.4	n.2904C>T		non_coding_transcript_exon_variant	Exon 4 of 4
LOC102723576	XR_939020.3	n.1413+1491C>T		intron_variant	Intron 4 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000299279	ENST00000762194.1	n.506+1491C>T		intron_variant	Intron 4 of 4
ENSG00000299279	ENST00000762195.1	n.378+1491C>T		intron_variant	Intron 4 of 4
ENSG00000299279	ENST00000762196.1	n.621+1491C>T		intron_variant	Intron 4 of 4
ENSG00000299279	ENST00000762198.1	n.233+1491C>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes Cov.: 33

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

GnomAD4 genome Cov.: 33

Alfa AF: 0.00 Hom.: 481

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.15
DANN	Benign	0.84
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs10516439; hg19: chr4-100303158;