chr8-24924066-G-C

Variant names:

• chr8-24924066-G-C
• rs1379357
• ENST00000781717.1:n.222+524C>G

Variant summary

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

The ENST00000781717.1(ENSG00000301773):​n.222+524C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.526 in 152,054 control chromosomes in the GnomAD database, including 24,321 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 0.53 (24321 hom., cov: 32)
• Consequence: ENSG00000301773 ENST00000781717.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0510
• Publications: 4 publications found

Genes affected

ENSG00000301773 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.669 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC112268023	XR_002956698.2	n.121+524C>G		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000301773	ENST00000781717.1	n.222+524C>G		intron_variant	Intron 2 of 2
ENSG00000301773	ENST00000781718.1	n.294+524C>G		intron_variant	Intron 2 of 3
ENSG00000301773	ENST00000781719.1	n.137-3131C>G		intron_variant	Intron 1 of 2
ENSG00000301773	ENST00000781720.1	n.298+524C>G		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.527 AC: 80024 AN: 151936 Hom.: 24311 Cov.: 32

Gnomad AFR AF: 0.198

Gnomad AMI AF: 0.575

Gnomad AMR AF: 0.680

Gnomad ASJ AF: 0.561

Gnomad EAS AF: 0.587

Gnomad SAS AF: 0.664

Gnomad FIN AF: 0.629

Gnomad MID AF: 0.566

Gnomad NFE AF: 0.659

Gnomad OTH AF: 0.536

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

GnomAD4 genome AF: 0.526 AC: 80053 AN: 152054 Hom.: 24321 Cov.: 32 AF XY: 0.530 AC XY: 39401 AN XY: 74334

African (AFR) AF: 0.198 AC: 8190 AN: 41444

American (AMR) AF: 0.680 AC: 10397 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.561 AC: 1946 AN: 3470

East Asian (EAS) AF: 0.589 AC: 3038 AN: 5162

South Asian (SAS) AF: 0.663 AC: 3199 AN: 4822

European-Finnish (FIN) AF: 0.629 AC: 6638 AN: 10560

Middle Eastern (MID) AF: 0.582 AC: 171 AN: 294

European-Non Finnish (NFE) AF: 0.659 AC: 44816 AN: 67994

Other (OTH) AF: 0.537 AC: 1134 AN: 2110

Alfa AF: 0.577 Hom.: 3419

Bravo AF: 0.516

Asia WGS AF: 0.629 AC: 2185 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.0
DANN	Benign	0.36
PhyloP100		-0.051

Splicing

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

Other links and lift over

dbSNP: rs1379357; hg19: chr8-24781579;