rs10485388

Variant names:

• chr6-74101979-A-G
• rs10485388
• ENST00000435946.1:n.138+32391A>G

Variant summary

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

The ENST00000435946.1(ENSG00000223786):​n.138+32391A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.129 in 151,768 control chromosomes in the GnomAD database, including 1,299 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 0.13 (1299 hom., cov: 30)
• Consequence: ENSG00000223786 ENST00000435946.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.212
• Publications: 3 publications found

Genes affected

ENSG00000223786 (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 (NFE) allele frequency at 95% confidence interval = 0.148 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC101928516	NR_110856.1	n.138+32391A>G		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000223786	ENST00000435946.1	n.138+32391A>G		intron_variant	Intron 1 of 3	1

Frequencies

GnomAD3 genomes AF: 0.129 AC: 19576 AN: 151650 Hom.: 1300 Cov.: 30

Gnomad AFR AF: 0.126

Gnomad AMI AF: 0.189

Gnomad AMR AF: 0.0957

Gnomad ASJ AF: 0.0824

Gnomad EAS AF: 0.0902

Gnomad SAS AF: 0.0872

Gnomad FIN AF: 0.108

Gnomad MID AF: 0.0637

Gnomad NFE AF: 0.150

Gnomad OTH AF: 0.109

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

GnomAD4 genome AF: 0.129 AC: 19588 AN: 151768 Hom.: 1299 Cov.: 30 AF XY: 0.126 AC XY: 9362 AN XY: 74154

African (AFR) AF: 0.126 AC: 5200 AN: 41406

American (AMR) AF: 0.0958 AC: 1458 AN: 15218

Ashkenazi Jewish (ASJ) AF: 0.0824 AC: 286 AN: 3470

East Asian (EAS) AF: 0.0906 AC: 463 AN: 5112

South Asian (SAS) AF: 0.0872 AC: 418 AN: 4792

European-Finnish (FIN) AF: 0.108 AC: 1142 AN: 10568

Middle Eastern (MID) AF: 0.0651 AC: 19 AN: 292

European-Non Finnish (NFE) AF: 0.150 AC: 10202 AN: 67892

Other (OTH) AF: 0.108 AC: 228 AN: 2106

Alfa AF: 0.143 Hom.: 768

Bravo AF: 0.129

Asia WGS AF: 0.0840 AC: 292 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	4.3
DANN	Benign	0.29
PhyloP100		0.21
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs10485388; hg19: chr6-74811695;