10-121645966-C-G

Variant names:

• chr10-121645966-C-G
• rs7902581
• ENST00000779978.1:n.234-516G>C

Variant summary

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

The ENST00000779978.1(ENSG00000301578):​n.234-516G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.338 in 151,928 control chromosomes in the GnomAD database, including 9,551 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 0.34 (9551 hom., cov: 31)
• Consequence: ENSG00000301578 ENST00000779978.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.611
• Publications: 5 publications found

Genes affected

ENSG00000301578 (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 (AFR) allele frequency at 95% confidence interval = 0.503 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000779978.1. 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
	ENSG00000301578	ENST00000779978.1		n.234-516G>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.338 AC: 51325 AN: 151810 Hom.: 9539 Cov.: 31

Gnomad AFR AF: 0.509

Gnomad AMI AF: 0.111

Gnomad AMR AF: 0.291

Gnomad ASJ AF: 0.223

Gnomad EAS AF: 0.215

Gnomad SAS AF: 0.423

Gnomad FIN AF: 0.229

Gnomad MID AF: 0.348

Gnomad NFE AF: 0.274

Gnomad OTH AF: 0.336

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

GnomAD4 genome AF: 0.338 AC: 51374 AN: 151928 Hom.: 9551 Cov.: 31 AF XY: 0.335 AC XY: 24871 AN XY: 74276

African (AFR) AF: 0.509 AC: 21029 AN: 41338

American (AMR) AF: 0.291 AC: 4446 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.223 AC: 774 AN: 3466

East Asian (EAS) AF: 0.216 AC: 1110 AN: 5144

South Asian (SAS) AF: 0.422 AC: 2035 AN: 4822

European-Finnish (FIN) AF: 0.229 AC: 2425 AN: 10590

Middle Eastern (MID) AF: 0.347 AC: 102 AN: 294

European-Non Finnish (NFE) AF: 0.274 AC: 18648 AN: 67962

Other (OTH) AF: 0.333 AC: 704 AN: 2116

Alfa AF: 0.153 Hom.: 258

Bravo AF: 0.346

Asia WGS AF: 0.338 AC: 1175 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	3.0
DANN	Benign	0.62
PhyloP100		0.61

Splicing

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

Other links and lift over

dbSNP: rs7902581; hg19: chr10-123405480;