chr1-153023685-G-C

Variant names:

• chr1-153023685-G-C
• rs16834871
• ENST00000728833.1:n.319-258G>C

Variant summary

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

The ENST00000728833.1(ENSG00000295252):​n.319-258G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0378 in 152,092 control chromosomes in the GnomAD database, including 851 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 0.038 (851 hom., cov: 31)
• Consequence: ENSG00000295252 ENST00000728833.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.527
• Publications: 1 publications found

Genes affected

ENSG00000295252 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.47 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000728833.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000295252	ENST00000728833.1		n.319-258G>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0377 AC: 5731 AN: 151974 Hom.: 844 Cov.: 31

Gnomad AFR AF: 0.0111

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.106

Gnomad ASJ AF: 0.00779

Gnomad EAS AF: 0.486

Gnomad SAS AF: 0.200

Gnomad FIN AF: 0.000661

Gnomad MID AF: 0.00633

Gnomad NFE AF: 0.00169

Gnomad OTH AF: 0.0311

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

GnomAD4 genome AF: 0.0378 AC: 5753 AN: 152092 Hom.: 851 Cov.: 31 AF XY: 0.0443 AC XY: 3292 AN XY: 74326

African (AFR) AF: 0.0112 AC: 464 AN: 41512

American (AMR) AF: 0.106 AC: 1624 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.00779 AC: 27 AN: 3468

East Asian (EAS) AF: 0.486 AC: 2479 AN: 5104

South Asian (SAS) AF: 0.200 AC: 959 AN: 4800

European-Finnish (FIN) AF: 0.000661 AC: 7 AN: 10588

Middle Eastern (MID) AF: 0.00680 AC: 2 AN: 294

European-Non Finnish (NFE) AF: 0.00171 AC: 116 AN: 68026

Other (OTH) AF: 0.0355 AC: 75 AN: 2112

Alfa AF: 0.0157 Hom.: 29

Bravo AF: 0.0465

Asia WGS AF: 0.288 AC: 1002 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.2
DANN	Benign	0.61
PhyloP100		-0.53

Splicing

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

Other links and lift over

dbSNP: rs16834871; hg19: chr1-152996161;