chr16-11293103-C-T

Position:

• chr16-11293103-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000653530.1(ENSG00000287429):​n.190-1502C>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 0.0147 in 152,280 control chromosomes in the GnomAD database, including 26 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 0.015 (26 hom., cov: 32)
• Consequence: ENST00000653530.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.658

Genes affected

RMI2 (HGNC:28349): (RecQ mediated genome instability 2) RMI2 is a component of the BLM (RECQL3; MIM 604610) complex, which plays a role in homologous recombination-dependent DNA repair and is essential for genome stability (Xu et al., 2008 [PubMed 18923082]).[supplied by OMIM, Nov 2008]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BS1: Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0147 (2238/152280) while in subpopulation NFE AF= 0.0232 (1580/68024). AF 95% confidence interval is 0.0223. There are 26 homozygotes in gnomad4. There are 1076 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 26 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105371082	XR_933070.4	n.178+43325C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
RMI2	ENST00000572173.1	c.-515-2113C>T		intron_variant		1		ENSP00000461206
	ENST00000653530.1	n.190-1502C>T		intron_variant, non_coding_transcript_variant
RMI2	ENST00000573910.1	n.161-23349C>T		intron_variant, non_coding_transcript_variant		3
RMI2	ENST00000649869.1	n.152+43325C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0147 AC: 2238 AN: 152162 Hom.: 26 Cov.: 32

Gnomad AFR AF: 0.00391

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.00956

Gnomad ASJ AF: 0.000288

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00124

Gnomad FIN AF: 0.0299

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0232

Gnomad OTH AF: 0.0120

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

GnomAD4 genome AF: 0.0147 AC: 2238 AN: 152280 Hom.: 26 Cov.: 32 AF XY: 0.0145 AC XY: 1076 AN XY: 74452

Gnomad4 AFR AF: 0.00390

Gnomad4 AMR AF: 0.00954

Gnomad4 ASJ AF: 0.000288

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00124

Gnomad4 FIN AF: 0.0299

Gnomad4 NFE AF: 0.0232

Gnomad4 OTH AF: 0.0118

Alfa AF: 0.00838 Hom.: 0

Bravo AF: 0.0131

Asia WGS AF: 0.00202 AC: 7 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.7
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs117096873; hg19: chr16-11386960;