chr5-117208476-C-A

Variant names:

• chr5-117208476-C-A
• rs1021516
• ENST00000762615.1:n.315+6434G>T

Variant summary

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

The ENST00000762615.1(ENSG00000299327):​n.315+6434G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.514 in 152,068 control chromosomes in the GnomAD database, including 23,339 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 0.51 (23339 hom., cov: 32)
• Consequence: ENSG00000299327 ENST00000762615.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.07
• Publications: 4 publications found

Genes affected

ENSG00000299327 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.812 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
ENSG00000299327	ENST00000762615.1	n.315+6434G>T		intron_variant	Intron 3 of 3
ENSG00000299327	ENST00000762616.1	n.185+6434G>T		intron_variant	Intron 2 of 2
ENSG00000299365	ENST00000762878.1	n.249-375C>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.514 AC: 78062 AN: 151950 Hom.: 23294 Cov.: 32

Gnomad AFR AF: 0.819

Gnomad AMI AF: 0.596

Gnomad AMR AF: 0.429

Gnomad ASJ AF: 0.483

Gnomad EAS AF: 0.0940

Gnomad SAS AF: 0.341

Gnomad FIN AF: 0.333

Gnomad MID AF: 0.538

Gnomad NFE AF: 0.420

Gnomad OTH AF: 0.500

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

GnomAD4 genome AF: 0.514 AC: 78163 AN: 152068 Hom.: 23339 Cov.: 32 AF XY: 0.503 AC XY: 37362 AN XY: 74306

African (AFR) AF: 0.819 AC: 33994 AN: 41498

American (AMR) AF: 0.429 AC: 6546 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.483 AC: 1676 AN: 3470

East Asian (EAS) AF: 0.0942 AC: 487 AN: 5170

South Asian (SAS) AF: 0.340 AC: 1635 AN: 4814

European-Finnish (FIN) AF: 0.333 AC: 3515 AN: 10556

Middle Eastern (MID) AF: 0.534 AC: 155 AN: 290

European-Non Finnish (NFE) AF: 0.420 AC: 28555 AN: 67984

Other (OTH) AF: 0.500 AC: 1056 AN: 2112

Alfa AF: 0.459 Hom.: 52265

Bravo AF: 0.533

Asia WGS AF: 0.273 AC: 951 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.11
DANN	Benign	0.36
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs1021516; hg19: chr5-116544172;