16-11257108-G-A

Position:

• chr16-11257108-G-A

Variant summary

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

The XR_933070.4(LOC105371082):​n.178+7330G>A 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 0.214 in 152,000 control chromosomes in the GnomAD database, including 3,623 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 0.21 (3623 hom., cov: 31)
• Consequence: LOC105371082 XR_933070.4 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0660

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]

LOC105371082 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.24 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105371082	XR_933070.4	n.178+7330G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
RMI2	ENST00000572173.1	c.-516+7330G>A		intron_variant		1		ENSP00000461206
RMI2	ENST00000573910.1	n.160+7330G>A		intron_variant, non_coding_transcript_variant		3
RMI2	ENST00000649869.1	n.152+7330G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.214 AC: 32476 AN: 151882 Hom.: 3622 Cov.: 31

Gnomad AFR AF: 0.213

Gnomad AMI AF: 0.161

Gnomad AMR AF: 0.177

Gnomad ASJ AF: 0.191

Gnomad EAS AF: 0.00848

Gnomad SAS AF: 0.144

Gnomad FIN AF: 0.228

Gnomad MID AF: 0.222

Gnomad NFE AF: 0.243

Gnomad OTH AF: 0.219

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

GnomAD4 genome AF: 0.214 AC: 32471 AN: 152000 Hom.: 3623 Cov.: 31 AF XY: 0.210 AC XY: 15611 AN XY: 74296

Gnomad4 AFR AF: 0.213

Gnomad4 AMR AF: 0.176

Gnomad4 ASJ AF: 0.191

Gnomad4 EAS AF: 0.00869

Gnomad4 SAS AF: 0.143

Gnomad4 FIN AF: 0.228

Gnomad4 NFE AF: 0.243

Gnomad4 OTH AF: 0.218

Alfa AF: 0.226 Hom.: 8337

Bravo AF: 0.208

Asia WGS AF: 0.109 AC: 380 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	5.3
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs193779; hg19: chr16-11350965;