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. The variant received -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
• Publications: 3 publications found

Genes affected

ENSG00000259283 (HGNC:):

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000558730.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000259283	ENST00000558730.2	TSL:3	n.89-8546G>T		intron	N/A
	RN7SL841P	ENST00000470547.3	TSL:6	n.*169G>T		downstream_gene	N/A

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

African (AFR) AF: 0.386 AC: 16003 AN: 41458

American (AMR) AF: 0.372 AC: 5673 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.297 AC: 1032 AN: 3472

East Asian (EAS) AF: 0.668 AC: 3442 AN: 5156

South Asian (SAS) AF: 0.452 AC: 2177 AN: 4812

European-Finnish (FIN) AF: 0.347 AC: 3665 AN: 10558

Middle Eastern (MID) AF: 0.367 AC: 108 AN: 294

European-Non Finnish (NFE) AF: 0.324 AC: 22029 AN: 67956

Other (OTH) AF: 0.370 AC: 781 AN: 2108

Alfa AF: 0.322 Hom.: 9848

Bravo AF: 0.370

Asia WGS AF: 0.560 AC: 1946 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	1.9
DANN	Benign	0.78
PhyloP100		-0.048

Splicing

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

Other links and lift over

dbSNP: rs748005; hg19: chr16-55325122;