10-100101678-G-A

Variant names:

• chr10-100101678-G-A
• rs11597390
• ENST00000807894.1:n.430+5441G>A

Variant summary

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

The ENST00000807894.1(ENSG00000305032):​n.430+5441G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.291 in 151,956 control chromosomes in the GnomAD database, including 6,987 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 0.29 (6987 hom., cov: 32)
• Consequence: ENSG00000305032 ENST00000807894.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.16
• Publications: 48 publications found

Genes affected

ENSG00000305032 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.356 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000807894.1. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000305032	ENST00000807894.1		n.430+5441G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.291 AC: 44204 AN: 151838 Hom.: 6977 Cov.: 32

Gnomad AFR AF: 0.202

Gnomad AMI AF: 0.351

Gnomad AMR AF: 0.349

Gnomad ASJ AF: 0.292

Gnomad EAS AF: 0.0678

Gnomad SAS AF: 0.148

Gnomad FIN AF: 0.279

Gnomad MID AF: 0.323

Gnomad NFE AF: 0.359

Gnomad OTH AF: 0.321

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

GnomAD4 genome AF: 0.291 AC: 44239 AN: 151956 Hom.: 6987 Cov.: 32 AF XY: 0.286 AC XY: 21224 AN XY: 74248

African (AFR) AF: 0.202 AC: 8379 AN: 41440

American (AMR) AF: 0.349 AC: 5328 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.292 AC: 1013 AN: 3470

East Asian (EAS) AF: 0.0674 AC: 349 AN: 5178

South Asian (SAS) AF: 0.148 AC: 714 AN: 4818

European-Finnish (FIN) AF: 0.279 AC: 2939 AN: 10526

Middle Eastern (MID) AF: 0.316 AC: 93 AN: 294

European-Non Finnish (NFE) AF: 0.359 AC: 24424 AN: 67960

Other (OTH) AF: 0.322 AC: 681 AN: 2112

Alfa AF: 0.333 Hom.: 23677

Bravo AF: 0.296

Asia WGS AF: 0.128 AC: 449 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	0.029
DANN	Benign	0.67
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs11597390; hg19: chr10-101861435;