rs251934

Variant names:

• chr5-175351675-A-G
• rs251934
• ENST00000820924.1:n.419+1769A>G

Variant summary

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

The ENST00000820924.1(ENSG00000306776):​n.419+1769A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.339 in 152,064 control chromosomes in the GnomAD database, including 9,321 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 0.34 (9321 hom., cov: 32)
• Consequence: ENSG00000306776 ENST00000820924.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.450
• Publications: 17 publications found

Genes affected

ENSG00000306776 (HGNC:):

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 (NFE) allele frequency at 95% confidence interval = 0.403 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
ENSG00000306776	ENST00000820924.1	n.419+1769A>G		intron_variant	Intron 2 of 2
ENSG00000306776	ENST00000820925.1	n.272+4098A>G		intron_variant	Intron 1 of 1
ENSG00000306776	ENST00000820926.1	n.272+4098A>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.339 AC: 51446 AN: 151946 Hom.: 9314 Cov.: 32

Gnomad AFR AF: 0.232

Gnomad AMI AF: 0.354

Gnomad AMR AF: 0.344

Gnomad ASJ AF: 0.383

Gnomad EAS AF: 0.129

Gnomad SAS AF: 0.281

Gnomad FIN AF: 0.413

Gnomad MID AF: 0.377

Gnomad NFE AF: 0.407

Gnomad OTH AF: 0.370

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

GnomAD4 genome AF: 0.339 AC: 51474 AN: 152064 Hom.: 9321 Cov.: 32 AF XY: 0.335 AC XY: 24916 AN XY: 74318

African (AFR) AF: 0.232 AC: 9633 AN: 41490

American (AMR) AF: 0.343 AC: 5242 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.383 AC: 1326 AN: 3466

East Asian (EAS) AF: 0.130 AC: 669 AN: 5162

South Asian (SAS) AF: 0.282 AC: 1361 AN: 4818

European-Finnish (FIN) AF: 0.413 AC: 4366 AN: 10564

Middle Eastern (MID) AF: 0.381 AC: 112 AN: 294

European-Non Finnish (NFE) AF: 0.407 AC: 27661 AN: 67974

Other (OTH) AF: 0.370 AC: 781 AN: 2110

Alfa AF: 0.359 Hom.: 8532

Bravo AF: 0.326

Asia WGS AF: 0.210 AC: 736 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.2
DANN	Benign	0.55
PhyloP100		-0.45

Splicing

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

Other links and lift over

dbSNP: rs251934; hg19: chr5-174778678; COSMIC: COSV50192838;