rs10112245

Variant names:

• chr8-5279535-A-C
• rs10112245
• ENST00000778535.1:n.123+9246T>G

Your query was ambiguous. Multiple possible variants found:

• chr8-5279535-A-C
• chr8-5279535-A-T

Variant summary

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

The ENST00000778535.1(ENSG00000301371):​n.123+9246T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.113 in 152,168 control chromosomes in the GnomAD database, including 1,007 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 0.11 (1007 hom., cov: 33)
• Consequence: ENSG00000301371 ENST00000778535.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0490
• Publications: 2 publications found

Genes affected

ENSG00000301371 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.125 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
ENSG00000301371	ENST00000778535.1	n.123+9246T>G		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.113 AC: 17125 AN: 152050 Hom.: 1005 Cov.: 33

Gnomad AFR AF: 0.0986

Gnomad AMI AF: 0.0559

Gnomad AMR AF: 0.0837

Gnomad ASJ AF: 0.169

Gnomad EAS AF: 0.0807

Gnomad SAS AF: 0.0790

Gnomad FIN AF: 0.136

Gnomad MID AF: 0.169

Gnomad NFE AF: 0.127

Gnomad OTH AF: 0.103

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

GnomAD4 genome AF: 0.113 AC: 17131 AN: 152168 Hom.: 1007 Cov.: 33 AF XY: 0.111 AC XY: 8278 AN XY: 74384

African (AFR) AF: 0.0985 AC: 4091 AN: 41530

American (AMR) AF: 0.0835 AC: 1276 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.169 AC: 585 AN: 3470

East Asian (EAS) AF: 0.0807 AC: 418 AN: 5182

South Asian (SAS) AF: 0.0791 AC: 381 AN: 4816

European-Finnish (FIN) AF: 0.136 AC: 1435 AN: 10580

Middle Eastern (MID) AF: 0.154 AC: 45 AN: 292

European-Non Finnish (NFE) AF: 0.127 AC: 8625 AN: 67998

Other (OTH) AF: 0.106 AC: 224 AN: 2114

Alfa AF: 0.119 Hom.: 1661

Bravo AF: 0.109

Asia WGS AF: 0.0920 AC: 319 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.65
DANN	Benign	0.78
PhyloP100		0.049

Splicing

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

Other links and lift over

dbSNP: rs10112245; hg19: chr8-5137057;