rs1059996

Variant names:

• chr17-47048219-C-T
• rs1059996
• ENST00000658121.1:n.8656G>A

Variant summary

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

The ENST00000658121.1(ENSG00000262879):​n.8656G>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: 25)
• Consequence: ENSG00000262879 ENST00000658121.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.918
• Publications: 1 publications found

Genes affected

ENSG00000262879 (HGNC:58690):

LOC101927060 (HGNC:):

LRRC37A17P (HGNC:48365): (leucine rich repeat containing 37 member A17, pseudogene)

LRRC37A2 (HGNC:32404): (leucine rich repeat containing 37 member A2) Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

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=-0.97).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC101927060	XR_007065785.1	n.13407G>A		non_coding_transcript_exon_variant	Exon 5 of 5
LRRC37A17P		n.47048219C>T		intragenic_variant
LRRC37A2	XM_024450773.2	c.4810-837C>T		intron_variant	Intron 10 of 10		XP_024306541.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000262879	ENST00000658121.1	n.8656G>A		non_coding_transcript_exon_variant	Exon 2 of 2
ENSG00000262879	ENST00000722962.1	n.1224G>A		non_coding_transcript_exon_variant	Exon 4 of 4
ENSG00000262879	ENST00000722972.1	n.1512G>A		non_coding_transcript_exon_variant	Exon 2 of 2

Frequencies

GnomAD3 genomes Cov.: 25

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

GnomAD4 genome Cov.: 25

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.6
DANN	Benign	0.41
PhyloP100		-0.92

Splicing

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

Other links and lift over

dbSNP: rs1059996; hg19: chr17-45125585;