rs10246819

Variant names:

• chr7-137023221-T-C
• rs10246819
• ENST00000439694.6:n.655+8684A>G

Variant summary

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

The ENST00000439694.6(ENSG00000234352):​n.655+8684A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.556 in 151,576 control chromosomes in the GnomAD database, including 24,805 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 0.56 (24805 hom., cov: 32)
• Consequence: ENSG00000234352 ENST00000439694.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.02
• Publications: 2 publications found

Genes affected

ENSG00000234352 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.685 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC349160	NR_046103.1	n.341+9573A>G		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000234352	ENST00000439694.6	n.655+8684A>G		intron_variant	Intron 3 of 3	1
ENSG00000234352	ENST00000425981.2	n.341+9573A>G		intron_variant	Intron 2 of 3	2
ENSG00000234352	ENST00000586239.5	n.273+9573A>G		intron_variant	Intron 2 of 4	5

Frequencies

GnomAD3 genomes AF: 0.556 AC: 84170 AN: 151458 Hom.: 24774 Cov.: 32

Gnomad AFR AF: 0.692

Gnomad AMI AF: 0.567

Gnomad AMR AF: 0.430

Gnomad ASJ AF: 0.577

Gnomad EAS AF: 0.102

Gnomad SAS AF: 0.248

Gnomad FIN AF: 0.615

Gnomad MID AF: 0.602

Gnomad NFE AF: 0.546

Gnomad OTH AF: 0.556

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

GnomAD4 genome AF: 0.556 AC: 84239 AN: 151576 Hom.: 24805 Cov.: 32 AF XY: 0.550 AC XY: 40703 AN XY: 74064

African (AFR) AF: 0.692 AC: 28644 AN: 41402

American (AMR) AF: 0.429 AC: 6525 AN: 15194

Ashkenazi Jewish (ASJ) AF: 0.577 AC: 2001 AN: 3470

East Asian (EAS) AF: 0.102 AC: 523 AN: 5116

South Asian (SAS) AF: 0.248 AC: 1196 AN: 4820

European-Finnish (FIN) AF: 0.615 AC: 6466 AN: 10506

Middle Eastern (MID) AF: 0.603 AC: 176 AN: 292

European-Non Finnish (NFE) AF: 0.547 AC: 37036 AN: 67766

Other (OTH) AF: 0.550 AC: 1158 AN: 2104

Alfa AF: 0.537 Hom.: 10310

Bravo AF: 0.551

Asia WGS AF: 0.235 AC: 810 AN: 3436

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.49
DANN	Benign	0.60
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs10246819; hg19: chr7-136707968;