chr1-221541794-C-T

Variant names:

• chr1-221541794-C-T
• rs11118748
• ENST00000775179.1:n.280-12293C>T

Variant summary

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

The ENST00000775179.1(ENSG00000286398):​n.280-12293C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0515 in 152,224 control chromosomes in the GnomAD database, including 311 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 0.052 (311 hom., cov: 32)
• Consequence: ENSG00000286398 ENST00000775179.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.47
• Publications: 1 publications found

Genes affected

ENSG00000286398 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.111 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
ENSG00000286398	ENST00000775179.1	n.280-12293C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.0514 AC: 7824 AN: 152106 Hom.: 309 Cov.: 32

Gnomad AFR AF: 0.113

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0343

Gnomad ASJ AF: 0.0279

Gnomad EAS AF: 0.0549

Gnomad SAS AF: 0.0549

Gnomad FIN AF: 0.0155

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.0251

Gnomad OTH AF: 0.0402

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

GnomAD4 genome AF: 0.0515 AC: 7844 AN: 152224 Hom.: 311 Cov.: 32 AF XY: 0.0497 AC XY: 3698 AN XY: 74410

African (AFR) AF: 0.113 AC: 4705 AN: 41530

American (AMR) AF: 0.0342 AC: 523 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0279 AC: 97 AN: 3472

East Asian (EAS) AF: 0.0548 AC: 284 AN: 5178

South Asian (SAS) AF: 0.0548 AC: 264 AN: 4820

European-Finnish (FIN) AF: 0.0155 AC: 164 AN: 10600

Middle Eastern (MID) AF: 0.0374 AC: 11 AN: 294

European-Non Finnish (NFE) AF: 0.0251 AC: 1710 AN: 68014

Other (OTH) AF: 0.0407 AC: 86 AN: 2114

Alfa AF: 0.0332 Hom.: 143

Bravo AF: 0.0545

Asia WGS AF: 0.0590 AC: 205 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.081
DANN	Benign	0.44
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs11118748; hg19: chr1-221715136;