rs238099

Variant names:

• chr1-229373158-T-C
• rs238099
• ENST00000733955.1:n.273-11055T>C

Your query was ambiguous. Multiple possible variants found:

• chr1-229373158-T-C
• chr1-229373158-T-G

Variant summary

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

The ENST00000733955.1(ENSG00000295926):​n.273-11055T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.383 in 151,938 control chromosomes in the GnomAD database, including 12,567 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 0.38 (12567 hom., cov: 32)
• Consequence: ENSG00000295926 ENST00000733955.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.453
• Publications: 2 publications found

Genes affected

ENSG00000295926 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.693 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
ENSG00000295926	ENST00000733955.1	n.273-11055T>C		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.383 AC: 58130 AN: 151820 Hom.: 12571 Cov.: 32

Gnomad AFR AF: 0.191

Gnomad AMI AF: 0.482

Gnomad AMR AF: 0.390

Gnomad ASJ AF: 0.614

Gnomad EAS AF: 0.712

Gnomad SAS AF: 0.661

Gnomad FIN AF: 0.380

Gnomad MID AF: 0.563

Gnomad NFE AF: 0.438

Gnomad OTH AF: 0.422

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

GnomAD4 genome AF: 0.383 AC: 58143 AN: 151938 Hom.: 12567 Cov.: 32 AF XY: 0.387 AC XY: 28737 AN XY: 74226

African (AFR) AF: 0.191 AC: 7921 AN: 41436

American (AMR) AF: 0.390 AC: 5956 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.614 AC: 2129 AN: 3470

East Asian (EAS) AF: 0.712 AC: 3669 AN: 5152

South Asian (SAS) AF: 0.661 AC: 3189 AN: 4824

European-Finnish (FIN) AF: 0.380 AC: 4009 AN: 10546

Middle Eastern (MID) AF: 0.571 AC: 168 AN: 294

European-Non Finnish (NFE) AF: 0.438 AC: 29770 AN: 67936

Other (OTH) AF: 0.423 AC: 892 AN: 2110

Alfa AF: 0.433 Hom.: 56315

Bravo AF: 0.372

Asia WGS AF: 0.591 AC: 2055 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	7.2
DANN	Benign	0.56
PhyloP100		0.45

Splicing

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

Other links and lift over

dbSNP: rs238099; hg19: chr1-229508905;