rs2165953

chr10-4674350-G-Achr10-4674350-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_024475.1(MANCR):n.22+3699C>T variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.699 in 152,094 control chromosomes in the GnomAD database, including 38,577 homozygotes. 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: 𝑓 0.70 (38577 hom., cov: 33)
• Consequence: MANCR NR_024475.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.324

Genes affected

MANCR (HGNC:44678): (mitotically associated long non coding RNA)

LINC00705 (HGNC:27874): (long intergenic non-protein coding RNA 705)

LOC105376373 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.854 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MANCR	NR_024475.1	n.22+3699C>T		intron_variant, non_coding_transcript_variant
LOC105376373	XR_001747338.2	n.130-2315G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC00705	ENST00000665287.1	n.989-2315G>A		intron_variant, non_coding_transcript_variant
MANCR	ENST00000700874.1	n.168+3699C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.699 AC: 106245 AN: 151974 Hom.: 38574 Cov.: 33

Gnomad AFR AF: 0.482

Gnomad AMI AF: 0.756

Gnomad AMR AF: 0.790

Gnomad ASJ AF: 0.728

Gnomad EAS AF: 0.876

Gnomad SAS AF: 0.792

Gnomad FIN AF: 0.796

Gnomad MID AF: 0.706

Gnomad NFE AF: 0.773

Gnomad OTH AF: 0.700

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

GnomAD4 genome AF: 0.699 AC: 106278 AN: 152094 Hom.: 38577 Cov.: 33 AF XY: 0.704 AC XY: 52385 AN XY: 74368

Gnomad4 AFR AF: 0.482

Gnomad4 AMR AF: 0.790

Gnomad4 ASJ AF: 0.728

Gnomad4 EAS AF: 0.876

Gnomad4 SAS AF: 0.793

Gnomad4 FIN AF: 0.796

Gnomad4 NFE AF: 0.773

Gnomad4 OTH AF: 0.696

Alfa AF: 0.755 Hom.: 66365

Bravo AF: 0.688

Asia WGS AF: 0.822 AC: 2854 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	0.16
Dann	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2165953; hg19: chr10-4716542;