rs211004

Variant names:

• chr5-162217792-G-A
• rs211004
• ENST00000819933.1:n.147-5517C>T

Variant summary

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

The ENST00000819933.1(ENSG00000306643):​n.147-5517C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.293 in 151,962 control chromosomes in the GnomAD database, including 6,963 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 0.29 (6963 hom., cov: 32)
• Consequence: ENSG00000306643 ENST00000819933.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.02
• Publications: 0 publications found

Genes affected

ENSG00000306643 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.561 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
ENSG00000306643	ENST00000819933.1	n.147-5517C>T		intron_variant	Intron 2 of 3
ENSG00000306643	ENST00000819934.1	n.188-5517C>T		intron_variant	Intron 3 of 4
ENSG00000306643	ENST00000819935.1	n.110-2063C>T		intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes AF: 0.293 AC: 44519 AN: 151840 Hom.: 6956 Cov.: 32

Gnomad AFR AF: 0.335

Gnomad AMI AF: 0.360

Gnomad AMR AF: 0.261

Gnomad ASJ AF: 0.248

Gnomad EAS AF: 0.579

Gnomad SAS AF: 0.294

Gnomad FIN AF: 0.277

Gnomad MID AF: 0.269

Gnomad NFE AF: 0.258

Gnomad OTH AF: 0.260

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

GnomAD4 genome AF: 0.293 AC: 44561 AN: 151962 Hom.: 6963 Cov.: 32 AF XY: 0.295 AC XY: 21909 AN XY: 74268

African (AFR) AF: 0.335 AC: 13898 AN: 41432

American (AMR) AF: 0.260 AC: 3971 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.248 AC: 859 AN: 3462

East Asian (EAS) AF: 0.578 AC: 2975 AN: 5148

South Asian (SAS) AF: 0.295 AC: 1417 AN: 4804

European-Finnish (FIN) AF: 0.277 AC: 2921 AN: 10562

Middle Eastern (MID) AF: 0.248 AC: 73 AN: 294

European-Non Finnish (NFE) AF: 0.258 AC: 17564 AN: 67966

Other (OTH) AF: 0.263 AC: 555 AN: 2112

Alfa AF: 0.288 Hom.: 827

Bravo AF: 0.293

Asia WGS AF: 0.406 AC: 1410 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.38
DANN	Benign	0.68
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs211004; hg19: chr5-161644798;