10-100342375-G-C

Variant names:

• chr10-100342375-G-C
• rs11190478
• ENST00000429420.1:n.211+350C>G

Variant summary

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

The ENST00000429420.1(ENSG00000231188):​n.211+350C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.45 in 151,974 control chromosomes in the GnomAD database, including 16,109 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 0.45 (16109 hom., cov: 32)
• Consequence: ENSG00000231188 ENST00000429420.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.07
• Publications: 6 publications found

Genes affected

ENSG00000231188 (HGNC:58401):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.593 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
ENSG00000231188	ENST00000429420.1	n.211+350C>G		intron_variant	Intron 2 of 3	3

Frequencies

GnomAD3 genomes AF: 0.450 AC: 68302 AN: 151856 Hom.: 16095 Cov.: 32

Gnomad AFR AF: 0.599

Gnomad AMI AF: 0.469

Gnomad AMR AF: 0.382

Gnomad ASJ AF: 0.342

Gnomad EAS AF: 0.382

Gnomad SAS AF: 0.463

Gnomad FIN AF: 0.458

Gnomad MID AF: 0.398

Gnomad NFE AF: 0.383

Gnomad OTH AF: 0.434

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

GnomAD4 genome AF: 0.450 AC: 68362 AN: 151974 Hom.: 16109 Cov.: 32 AF XY: 0.454 AC XY: 33737 AN XY: 74288

African (AFR) AF: 0.599 AC: 24828 AN: 41444

American (AMR) AF: 0.381 AC: 5811 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.342 AC: 1186 AN: 3468

East Asian (EAS) AF: 0.382 AC: 1971 AN: 5166

South Asian (SAS) AF: 0.465 AC: 2234 AN: 4806

European-Finnish (FIN) AF: 0.458 AC: 4832 AN: 10558

Middle Eastern (MID) AF: 0.401 AC: 117 AN: 292

European-Non Finnish (NFE) AF: 0.383 AC: 26044 AN: 67976

Other (OTH) AF: 0.434 AC: 913 AN: 2104

Alfa AF: 0.284 Hom.: 747

Bravo AF: 0.445

Asia WGS AF: 0.437 AC: 1520 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.61
DANN	Benign	0.32
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs11190478; hg19: chr10-102102132;