rs648119

Variant names:

• chr8-102125817-A-G
• rs648119
• ENST00000849392.1:n.115+25038A>G

Your query was ambiguous. Multiple possible variants found:

• chr8-102125817-A-G
• chr8-102125817-A-T

Variant summary

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

The ENST00000849392.1(ENSG00000310378):​n.115+25038A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.491 in 151,786 control chromosomes in the GnomAD database, including 18,687 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 0.49 (18687 hom., cov: 30)
• Consequence: ENSG00000310378 ENST00000849392.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.388
• Publications: 4 publications found

Genes affected

ENSG00000310378 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.541 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
ENSG00000310378	ENST00000849392.1	n.115+25038A>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.491 AC: 74517 AN: 151668 Hom.: 18676 Cov.: 30

Gnomad AFR AF: 0.442

Gnomad AMI AF: 0.476

Gnomad AMR AF: 0.390

Gnomad ASJ AF: 0.465

Gnomad EAS AF: 0.434

Gnomad SAS AF: 0.464

Gnomad FIN AF: 0.530

Gnomad MID AF: 0.437

Gnomad NFE AF: 0.546

Gnomad OTH AF: 0.488

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

GnomAD4 genome AF: 0.491 AC: 74569 AN: 151786 Hom.: 18687 Cov.: 30 AF XY: 0.487 AC XY: 36143 AN XY: 74156

African (AFR) AF: 0.442 AC: 18304 AN: 41378

American (AMR) AF: 0.390 AC: 5950 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.465 AC: 1613 AN: 3472

East Asian (EAS) AF: 0.434 AC: 2218 AN: 5116

South Asian (SAS) AF: 0.466 AC: 2236 AN: 4800

European-Finnish (FIN) AF: 0.530 AC: 5577 AN: 10528

Middle Eastern (MID) AF: 0.442 AC: 130 AN: 294

European-Non Finnish (NFE) AF: 0.546 AC: 37080 AN: 67912

Other (OTH) AF: 0.489 AC: 1029 AN: 2106

Alfa AF: 0.519 Hom.: 33504

Bravo AF: 0.481

Asia WGS AF: 0.461 AC: 1607 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	6.0
DANN	Benign	0.64
PhyloP100		0.39

Splicing

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

Other links and lift over

dbSNP: rs648119; hg19: chr8-103138045;