rs748005

Variant names:

• chr16-55291210-C-A
• rs748005
• ENST00000558730.2:n.89-8546G>T

Your query was ambiguous. Multiple possible variants found:

• chr16-55291210-C-A
• chr16-55291210-C-G
• chr16-55291210-C-T

Variant summary

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

The ENST00000558730.2(ENSG00000259283):​n.89-8546G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.363 in 151,990 control chromosomes in the GnomAD database, including 10,392 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 0.36 (10392 hom., cov: 32)
• Consequence: ENSG00000259283 ENST00000558730.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0480

Genes affected

ENSG00000259283 (HGNC:):

RN7SL841P (HGNC:46857): (RNA, 7SL, cytoplasmic 841, pseudogene)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.649 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000259283	ENST00000558730.2	n.89-8546G>T		intron_variant	Intron 1 of 3	3
RN7SL841P	ENST00000470547.3	n.*169G>T		downstream_gene_variant		6

Frequencies

GnomAD3 genomes AF: 0.363 AC: 55203 AN: 151872 Hom.: 10379 Cov.: 32

Gnomad AFR AF: 0.386

Gnomad AMI AF: 0.366

Gnomad AMR AF: 0.371

Gnomad ASJ AF: 0.297

Gnomad EAS AF: 0.668

Gnomad SAS AF: 0.453

Gnomad FIN AF: 0.347

Gnomad MID AF: 0.386

Gnomad NFE AF: 0.324

Gnomad OTH AF: 0.366

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

GnomAD4 genome AF: 0.363 AC: 55243 AN: 151990 Hom.: 10392 Cov.: 32 AF XY: 0.367 AC XY: 27265 AN XY: 74296

Gnomad4 AFR AF: 0.386

Gnomad4 AMR AF: 0.372

Gnomad4 ASJ AF: 0.297

Gnomad4 EAS AF: 0.668

Gnomad4 SAS AF: 0.452

Gnomad4 FIN AF: 0.347

Gnomad4 NFE AF: 0.324

Gnomad4 OTH AF: 0.370

Alfa AF: 0.313 Hom.: 7094

Bravo AF: 0.370

Asia WGS AF: 0.560 AC: 1946 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	1.9
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs748005; hg19: chr16-55325122;