5-121839230-T-C

Variant names:

• chr5-121839230-T-C
• rs10519684
• ENST00000793240.1:n.409-7123A>G

Variant summary

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

The ENST00000793240.1(ENSG00000303256):​n.409-7123A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0547 in 152,200 control chromosomes in the GnomAD database, including 401 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 0.055 (401 hom., cov: 32)
• Consequence: ENSG00000303256 ENST00000793240.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.01
• Publications: 1 publications found

Genes affected

ENSG00000303256 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.127 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105379149	XR_001742862.1	n.98-1419T>C		intron_variant	Intron 1 of 3
LOC105379149	XR_948712.3	n.98-1419T>C		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000303256	ENST00000793240.1	n.409-7123A>G		intron_variant	Intron 1 of 2
ENSG00000303256	ENST00000793241.1	n.476-7123A>G		intron_variant	Intron 2 of 3
ENSG00000303256	ENST00000793242.1	n.367+12212A>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.0545 AC: 8293 AN: 152082 Hom.: 398 Cov.: 32

Gnomad AFR AF: 0.130

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0276

Gnomad ASJ AF: 0.0176

Gnomad EAS AF: 0.000577

Gnomad SAS AF: 0.0333

Gnomad FIN AF: 0.0370

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.0263

Gnomad OTH AF: 0.0445

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

GnomAD4 genome AF: 0.0547 AC: 8319 AN: 152200 Hom.: 401 Cov.: 32 AF XY: 0.0528 AC XY: 3928 AN XY: 74446

African (AFR) AF: 0.130 AC: 5389 AN: 41518

American (AMR) AF: 0.0276 AC: 421 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.0176 AC: 61 AN: 3470

East Asian (EAS) AF: 0.000578 AC: 3 AN: 5188

South Asian (SAS) AF: 0.0327 AC: 158 AN: 4830

European-Finnish (FIN) AF: 0.0370 AC: 393 AN: 10618

Middle Eastern (MID) AF: 0.0306 AC: 9 AN: 294

European-Non Finnish (NFE) AF: 0.0263 AC: 1791 AN: 67998

Other (OTH) AF: 0.0445 AC: 94 AN: 2110

Alfa AF: 0.0441 Hom.: 37

Bravo AF: 0.0574

Asia WGS AF: 0.0330 AC: 115 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.18
DANN	Benign	0.57
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs10519684; hg19: chr5-121174925;