chr10-100346031-G-A

Variant names:

• chr10-100346031-G-A
• rs11599710
• ENST00000429420.1:n.103+257C>T

Variant summary

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

The ENST00000429420.1(ENSG00000231188):​n.103+257C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0905 in 152,092 control chromosomes in the GnomAD database, including 678 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 0.091 (678 hom., cov: 32)
• Consequence: ENSG00000231188 ENST00000429420.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.317
• 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=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.143 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.103+257C>T		intron_variant	Intron 1 of 3	3
ENSG00000231188	ENST00000746873.1	n.*222C>T		downstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.0906 AC: 13763 AN: 151976 Hom.: 680 Cov.: 32

Gnomad AFR AF: 0.0856

Gnomad AMI AF: 0.0833

Gnomad AMR AF: 0.0657

Gnomad ASJ AF: 0.108

Gnomad EAS AF: 0.152

Gnomad SAS AF: 0.124

Gnomad FIN AF: 0.0809

Gnomad MID AF: 0.121

Gnomad NFE AF: 0.0929

Gnomad OTH AF: 0.0837

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

GnomAD4 genome AF: 0.0905 AC: 13766 AN: 152092 Hom.: 678 Cov.: 32 AF XY: 0.0901 AC XY: 6697 AN XY: 74342

African (AFR) AF: 0.0856 AC: 3551 AN: 41474

American (AMR) AF: 0.0655 AC: 1002 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.108 AC: 376 AN: 3468

East Asian (EAS) AF: 0.152 AC: 784 AN: 5164

South Asian (SAS) AF: 0.123 AC: 592 AN: 4820

European-Finnish (FIN) AF: 0.0809 AC: 857 AN: 10590

Middle Eastern (MID) AF: 0.127 AC: 37 AN: 292

European-Non Finnish (NFE) AF: 0.0929 AC: 6314 AN: 67970

Other (OTH) AF: 0.0837 AC: 177 AN: 2114

Alfa AF: 0.0891 Hom.: 369

Bravo AF: 0.0889

Asia WGS AF: 0.117 AC: 408 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	4.6
DANN	Benign	0.47
PhyloP100		0.32

Splicing

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

Other links and lift over

dbSNP: rs11599710; hg19: chr10-102105788;