5-181007216-G-A

Variant names:

• chr5-181007216-G-A
• rs4700774
• ENST00000766731.1:n.394+30716C>T

Variant summary

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

The ENST00000766731.1(ENSG00000299843):​n.394+30716C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.254 in 151,986 control chromosomes in the GnomAD database, including 5,312 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 0.25 (5312 hom., cov: 32)
  • Exomes 𝑓: 0.25 (0 hom.)
• Consequence: ENSG00000299843 ENST00000766731.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.200
• Publications: 12 publications found

Genes affected

ENSG00000299843 (HGNC:):

RNU6-1036P (HGNC:47999): (RNA, U6 small nuclear 1036, pseudogene)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.3 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000766731.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000299843	ENST00000766731.1		n.394+30716C>T		intron	N/A
	ENSG00000299843	ENST00000766732.1		n.363-1823C>T		intron	N/A
	RNU6-1036P	ENST00000383959.1	TSL:6	n.-65G>A		upstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.254 AC: 38594 AN: 151864 Hom.: 5303 Cov.: 32

Gnomad AFR AF: 0.164

Gnomad AMI AF: 0.368

Gnomad AMR AF: 0.307

Gnomad ASJ AF: 0.168

Gnomad EAS AF: 0.259

Gnomad SAS AF: 0.108

Gnomad FIN AF: 0.335

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.298

Gnomad OTH AF: 0.243

GnomAD4 exome AF: 0.250 AC: 1 AN: 4 Hom.: 0 AF XY: 0.00 AC XY: 0 AN XY: 2

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.500 AC: 1 AN: 2

Other (OTH) AF: 0.00 AC: 0 AN: 2

GnomAD4 genome AF: 0.254 AC: 38613 AN: 151982 Hom.: 5312 Cov.: 32 AF XY: 0.254 AC XY: 18894 AN XY: 74296

African (AFR) AF: 0.163 AC: 6775 AN: 41448

American (AMR) AF: 0.308 AC: 4692 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.168 AC: 584 AN: 3470

East Asian (EAS) AF: 0.260 AC: 1345 AN: 5170

South Asian (SAS) AF: 0.107 AC: 517 AN: 4818

European-Finnish (FIN) AF: 0.335 AC: 3536 AN: 10562

Middle Eastern (MID) AF: 0.156 AC: 46 AN: 294

European-Non Finnish (NFE) AF: 0.298 AC: 20276 AN: 67948

Other (OTH) AF: 0.241 AC: 508 AN: 2112

Alfa AF: 0.265 Hom.: 1943

Bravo AF: 0.248

Asia WGS AF: 0.184 AC: 642 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.3
DANN	Benign	0.44
PhyloP100		0.20
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs4700774; hg19: chr5-180434216;