rs990871

chr1-72358030-C-Gchr1-72358030-C-T

Variant summary

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

The ENST00000665984.1(ENSG00000286863):n.153+74625C>G variant causes a intron, non coding transcript 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: ENST00000665984.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.839

Genes affected

(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=-0.98).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105378797	XR_001737670.2	n.472+74625C>G		intron_variant, non_coding_transcript_variant
LOC105378797	XR_001737671.3	n.472+74625C>G		intron_variant, non_coding_transcript_variant
LOC105378797	XR_947505.3	n.472+74625C>G		intron_variant, non_coding_transcript_variant
LOC105378797	XR_947506.3	n.472+74625C>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000665984.1	n.153+74625C>G		intron_variant, non_coding_transcript_variant
	ENST00000653965.1	n.236+74625C>G		intron_variant, non_coding_transcript_variant
	ENST00000667836.1	n.227+74625C>G		intron_variant, non_coding_transcript_variant
	ENST00000688733.1	n.56+74625C>G		intron_variant, non_coding_transcript_variant

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	-0.98
Cadd	Benign	0.36
Dann	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs990871; hg19: chr1-72823713;