10-111598317-A-C

Variant names:

• chr10-111598317-A-C
• rs1336433
• ENST00000829409.1:n.116+36742T>G

Variant summary

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

The ENST00000829409.1(ENSG00000307856):​n.116+36742T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.418 in 151,910 control chromosomes in the GnomAD database, including 13,702 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 0.42 (13702 hom., cov: 32)
• Consequence: ENSG00000307856 ENST00000829409.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.49
• Publications: 2 publications found

Genes affected

ENSG00000307856 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.468 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000829409.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000307856	ENST00000829409.1		n.116+36742T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.418 AC: 63515 AN: 151792 Hom.: 13684 Cov.: 32

Gnomad AFR AF: 0.474

Gnomad AMI AF: 0.344

Gnomad AMR AF: 0.309

Gnomad ASJ AF: 0.480

Gnomad EAS AF: 0.183

Gnomad SAS AF: 0.409

Gnomad FIN AF: 0.451

Gnomad MID AF: 0.411

Gnomad NFE AF: 0.421

Gnomad OTH AF: 0.408

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

GnomAD4 genome AF: 0.418 AC: 63559 AN: 151910 Hom.: 13702 Cov.: 32 AF XY: 0.416 AC XY: 30902 AN XY: 74242

African (AFR) AF: 0.474 AC: 19616 AN: 41418

American (AMR) AF: 0.309 AC: 4709 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.480 AC: 1666 AN: 3470

East Asian (EAS) AF: 0.183 AC: 942 AN: 5156

South Asian (SAS) AF: 0.408 AC: 1965 AN: 4818

European-Finnish (FIN) AF: 0.451 AC: 4755 AN: 10532

Middle Eastern (MID) AF: 0.415 AC: 122 AN: 294

European-Non Finnish (NFE) AF: 0.421 AC: 28607 AN: 67944

Other (OTH) AF: 0.410 AC: 865 AN: 2110

Alfa AF: 0.319 Hom.: 1273

Bravo AF: 0.407

Asia WGS AF: 0.296 AC: 1031 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.97
DANN	Benign	0.77
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs1336433; hg19: chr10-113358075;