rs1211375

Variant names:

• chr16-190281-A-C
• rs1211375
• NM_201412.3:c.807-146T>G

Your query was ambiguous. Multiple possible variants found:

• chr16-190281-A-C
• chr16-190281-A-T

Variant summary

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

The NM_201412.3(LUC7L):​c.807-146T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.64 in 784,174 control chromosomes in the GnomAD database, including 162,383 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 0.66 (32714 hom., cov: 28)
  • Exomes 𝑓: 0.64 (129669 hom.)
• Consequence: LUC7L NM_201412.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.41
• Publications: 34 publications found

Genes affected

LUC7L (HGNC:6723): (LUC7 like) The LUC7L gene may represent a mammalian heterochromatic gene, encoding a putative RNA-binding protein similar to the yeast Luc7p subunit of the U1 snRNP splicing complex that is normally required for 5-prime splice site selection (Tufarelli et al., 2001 [PubMed 11170747]).[supplied by OMIM, Mar 2008]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.714 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LUC7L	NM_201412.3	c.807-146T>G		intron_variant	Intron 8 of 9	ENST00000293872.13	NP_958815.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LUC7L	ENST00000293872.13	c.807-146T>G		intron_variant	Intron 8 of 9	1	NM_201412.3	ENSP00000293872.8

Frequencies

GnomAD3 genomes AF: 0.655 AC: 99211 AN: 151386 Hom.: 32688 Cov.: 28

Gnomad AFR AF: 0.721

Gnomad AMI AF: 0.690

Gnomad AMR AF: 0.640

Gnomad ASJ AF: 0.606

Gnomad EAS AF: 0.515

Gnomad SAS AF: 0.651

Gnomad FIN AF: 0.609

Gnomad MID AF: 0.659

Gnomad NFE AF: 0.640

Gnomad OTH AF: 0.637

GnomAD4 exome AF: 0.637 AC: 402877 AN: 632670 Hom.: 129669 AF XY: 0.638 AC XY: 207853 AN XY: 325840

African (AFR) AF: 0.726 AC: 11225 AN: 15470

American (AMR) AF: 0.685 AC: 13995 AN: 20424

Ashkenazi Jewish (ASJ) AF: 0.607 AC: 9128 AN: 15040

East Asian (EAS) AF: 0.529 AC: 16954 AN: 32068

South Asian (SAS) AF: 0.655 AC: 33235 AN: 50730

European-Finnish (FIN) AF: 0.612 AC: 25817 AN: 42156

Middle Eastern (MID) AF: 0.625 AC: 2427 AN: 3882

European-Non Finnish (NFE) AF: 0.641 AC: 269699 AN: 420766

Other (OTH) AF: 0.635 AC: 20397 AN: 32134

GnomAD4 genome AF: 0.655 AC: 99290 AN: 151504 Hom.: 32714 Cov.: 28 AF XY: 0.651 AC XY: 48179 AN XY: 73992

African (AFR) AF: 0.721 AC: 29749 AN: 41268

American (AMR) AF: 0.640 AC: 9704 AN: 15172

Ashkenazi Jewish (ASJ) AF: 0.606 AC: 2103 AN: 3470

East Asian (EAS) AF: 0.514 AC: 2637 AN: 5126

South Asian (SAS) AF: 0.650 AC: 3124 AN: 4804

European-Finnish (FIN) AF: 0.609 AC: 6354 AN: 10434

Middle Eastern (MID) AF: 0.671 AC: 196 AN: 292

European-Non Finnish (NFE) AF: 0.640 AC: 43443 AN: 67918

Other (OTH) AF: 0.641 AC: 1351 AN: 2108

Alfa AF: 0.644 Hom.: 62970

Bravo AF: 0.661

Asia WGS AF: 0.616 AC: 2143 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	0.13
DANN	Benign	0.46
PhyloP100		-1.4
PromoterAI		0.021	Neutral
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs1211375; hg19: chr16-240280; COSMIC: COSV53460289; COSMIC: COSV53460289;