10-18871100-A-G

Variant names:

• chr10-18871100-A-G
• rs16917919
• ENST00000723466.1:n.344+34868A>G

Variant summary

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

The ENST00000723466.1(ENSG00000234244):​n.344+34868A>G 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 152,012 control chromosomes in the GnomAD database, including 8,767 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 (8767 hom., cov: 32)
• Consequence: ENSG00000234244 ENST00000723466.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.133
• Publications: 5 publications found

Genes affected

ENSG00000234244 (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 (EAS) allele frequency at 95% confidence interval = 0.375 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
ENSG00000234244	ENST00000723466.1	n.344+34868A>G		intron_variant	Intron 5 of 7
ENSG00000234244	ENST00000723467.1	n.305+34868A>G		intron_variant	Intron 4 of 6

Frequencies

GnomAD3 genomes AF: 0.338 AC: 51365 AN: 151890 Hom.: 8767 Cov.: 32

Gnomad AFR AF: 0.324

Gnomad AMI AF: 0.248

Gnomad AMR AF: 0.260

Gnomad ASJ AF: 0.297

Gnomad EAS AF: 0.389

Gnomad SAS AF: 0.308

Gnomad FIN AF: 0.318

Gnomad MID AF: 0.418

Gnomad NFE AF: 0.369

Gnomad OTH AF: 0.344

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

GnomAD4 genome AF: 0.338 AC: 51390 AN: 152012 Hom.: 8767 Cov.: 32 AF XY: 0.334 AC XY: 24807 AN XY: 74316

African (AFR) AF: 0.324 AC: 13425 AN: 41470

American (AMR) AF: 0.259 AC: 3958 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.297 AC: 1031 AN: 3468

East Asian (EAS) AF: 0.389 AC: 2011 AN: 5168

South Asian (SAS) AF: 0.307 AC: 1480 AN: 4814

European-Finnish (FIN) AF: 0.318 AC: 3359 AN: 10568

Middle Eastern (MID) AF: 0.429 AC: 126 AN: 294

European-Non Finnish (NFE) AF: 0.369 AC: 25056 AN: 67948

Other (OTH) AF: 0.342 AC: 718 AN: 2100

Alfa AF: 0.354 Hom.: 31213

Bravo AF: 0.332

Asia WGS AF: 0.303 AC: 1056 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	2.7
DANN	Benign	0.36
PhyloP100		0.13

Splicing

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

Other links and lift over

dbSNP: rs16917919; hg19: chr10-19160029;