16-11379799-T-C

Variant names:

• chr16-11379799-T-C
• rs7203055
• NM_001370704.1:c.9958+3843A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001370704.1(LOC400499):​c.9958+3843A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.322 in 152,142 control chromosomes in the GnomAD database, including 8,049 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 0.32 (8049 hom., cov: 33)
• Consequence: LOC400499 NM_001370704.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.664
• Publications: 8 publications found

Genes affected

LOC400499 (HGNC:0):

LOC105371082 (HGNC:):

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]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.353 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC400499	NM_001370704.1	c.9958+3843A>G		intron_variant	Intron 66 of 66	ENST00000696174.1	NP_001357633.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000188897	ENST00000696174.1	c.9958+3843A>G		intron_variant	Intron 66 of 66		NM_001370704.1	ENSP00000512464.1

Frequencies

GnomAD3 genomes AF: 0.322 AC: 48946 AN: 152024 Hom.: 8050 Cov.: 33

Gnomad AFR AF: 0.288

Gnomad AMI AF: 0.317

Gnomad AMR AF: 0.276

Gnomad ASJ AF: 0.369

Gnomad EAS AF: 0.288

Gnomad SAS AF: 0.334

Gnomad FIN AF: 0.294

Gnomad MID AF: 0.313

Gnomad NFE AF: 0.357

Gnomad OTH AF: 0.326

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

GnomAD4 genome AF: 0.322 AC: 48969 AN: 152142 Hom.: 8049 Cov.: 33 AF XY: 0.317 AC XY: 23581 AN XY: 74378

African (AFR) AF: 0.288 AC: 11940 AN: 41476

American (AMR) AF: 0.276 AC: 4218 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.369 AC: 1280 AN: 3470

East Asian (EAS) AF: 0.288 AC: 1491 AN: 5186

South Asian (SAS) AF: 0.333 AC: 1607 AN: 4820

European-Finnish (FIN) AF: 0.294 AC: 3116 AN: 10592

Middle Eastern (MID) AF: 0.316 AC: 93 AN: 294

European-Non Finnish (NFE) AF: 0.357 AC: 24249 AN: 68000

Other (OTH) AF: 0.326 AC: 686 AN: 2106

Alfa AF: 0.345 Hom.: 38839

Bravo AF: 0.318

Asia WGS AF: 0.276 AC: 960 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.0
DANN	Benign	0.31
PhyloP100		-0.66

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs7203055; hg19: chr16-11473656;