rs10519686

Variant names:

• chr5-121839994-C-A
• rs10519686
• ENST00000793240.1:n.409-7887G>T

Your query was ambiguous. Multiple possible variants found:

• chr5-121839994-C-A
• chr5-121839994-C-T

Variant summary

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

The ENST00000793240.1(ENSG00000303256):​n.409-7887G>T 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 152,108 control chromosomes in the GnomAD database, including 402 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 (402 hom., cov: 32)
• Consequence: ENSG00000303256 ENST00000793240.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.121
• Publications: 0 publications found

Genes affected

ENSG00000303256 (HGNC:59120):

LOC105379149 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.127 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000793240.1. 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
	ENSG00000303256	ENST00000793240.1		n.409-7887G>T		intron	N/A
	ENSG00000303256	ENST00000793241.1		n.475+7658G>T		intron	N/A
	ENSG00000303256	ENST00000793242.1		n.367+11448G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0545 AC: 8289 AN: 151990 Hom.: 399 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: 0.000579

Gnomad SAS AF: 0.0333

Gnomad FIN AF: 0.0372

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.0263

Gnomad OTH AF: 0.0442

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

GnomAD4 genome AF: 0.0547 AC: 8315 AN: 152108 Hom.: 402 Cov.: 32 AF XY: 0.0528 AC XY: 3926 AN XY: 74388

African (AFR) AF: 0.130 AC: 5384 AN: 41476

American (AMR) AF: 0.0276 AC: 422 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0176 AC: 61 AN: 3466

East Asian (EAS) AF: 0.000580 AC: 3 AN: 5170

South Asian (SAS) AF: 0.0327 AC: 158 AN: 4828

European-Finnish (FIN) AF: 0.0372 AC: 394 AN: 10586

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

European-Non Finnish (NFE) AF: 0.0263 AC: 1791 AN: 67982

Other (OTH) AF: 0.0442 AC: 93 AN: 2104

Alfa AF: 0.0203 Hom.: 10

Bravo AF: 0.0574

Asia WGS AF: 0.0330 AC: 116 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.43
DANN	Benign	0.28
PhyloP100		-0.12

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs10519686;

hg19: chr5-121175689;