rs757080

Variant names:

• chr11-61074762-T-A
• rs757080
• XR_007062690.1:n.1051T>A

Your query was ambiguous. Multiple possible variants found:

• chr11-61074762-T-A
• chr11-61074762-T-C
• chr11-61074762-T-G

Variant summary

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

The XR_007062690.1(LOC124902677):​n.1051T>A 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: 31)
• Consequence: LOC124902677 XR_007062690.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.431
• Publications: 5 publications found

Genes affected

LOC124902677 (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=-0.83).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124902677	XR_007062690.1	n.1051T>A		non_coding_transcript_exon_variant	Exon 1 of 2
LOC105369325	NR_188502.1	n.62+17535A>T		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000303405	ENST00000794255.1	n.135+17535A>T		intron_variant	Intron 1 of 1
ENSG00000303405	ENST00000794256.1	n.136-9806A>T		intron_variant	Intron 1 of 2
ENSG00000303405	ENST00000794257.1	n.132+17535A>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes Cov.: 31

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

GnomAD4 genome Cov.: 31

Alfa AF: 0.00 Hom.: 9455

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.88
DANN	Benign	0.74
PhyloP100		-0.43

Splicing

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

Other links and lift over

dbSNP: rs757080; hg19: chr11-60842234;