chr1-229347401-C-A

Variant names:

• chr1-229347401-C-A
• rs238102
• ENST00000733955.1:n.163+1659C>A

Variant summary

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

The ENST00000733955.1(ENSG00000295926):​n.163+1659C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.326 in 152,030 control chromosomes in the GnomAD database, including 8,358 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 0.33 (8358 hom., cov: 32)
• Consequence: ENSG00000295926 ENST00000733955.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.44
• Publications: 4 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=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.408 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.163+1659C>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.326 AC: 49499 AN: 151912 Hom.: 8341 Cov.: 32

Gnomad AFR AF: 0.397

Gnomad AMI AF: 0.298

Gnomad AMR AF: 0.309

Gnomad ASJ AF: 0.435

Gnomad EAS AF: 0.423

Gnomad SAS AF: 0.391

Gnomad FIN AF: 0.205

Gnomad MID AF: 0.364

Gnomad NFE AF: 0.287

Gnomad OTH AF: 0.343

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

GnomAD4 genome AF: 0.326 AC: 49561 AN: 152030 Hom.: 8358 Cov.: 32 AF XY: 0.323 AC XY: 23971 AN XY: 74320

African (AFR) AF: 0.397 AC: 16474 AN: 41460

American (AMR) AF: 0.309 AC: 4718 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.435 AC: 1511 AN: 3470

East Asian (EAS) AF: 0.423 AC: 2187 AN: 5168

South Asian (SAS) AF: 0.390 AC: 1877 AN: 4812

European-Finnish (FIN) AF: 0.205 AC: 2171 AN: 10566

Middle Eastern (MID) AF: 0.367 AC: 108 AN: 294

European-Non Finnish (NFE) AF: 0.287 AC: 19529 AN: 67968

Other (OTH) AF: 0.339 AC: 714 AN: 2108

Alfa AF: 0.307 Hom.: 31341

Bravo AF: 0.338

Asia WGS AF: 0.382 AC: 1324 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.28
DANN	Benign	0.63
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs238102; hg19: chr1-229483148; COSMIC: COSV52910428;