1-170600176-A-G

Variant names:

• chr1-170600176-A-G
• rs3903239
• ENST00000413005.1:n.162+1161A>G

Variant summary

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

The ENST00000413005.1(ENSG00000235303):​n.162+1161A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.36 in 152,018 control chromosomes in the GnomAD database, including 11,018 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 0.36 (11018 hom., cov: 32)
• Consequence: ENSG00000235303 ENST00000413005.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.423
• Publications: 61 publications found

Genes affected

ENSG00000235303 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.592 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000413005.1. 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
	ENSG00000235303	ENST00000413005.1	TSL:2	n.162+1161A>G		intron	N/A
	ENSG00000235303	ENST00000835148.1		n.273+16986A>G		intron	N/A
	ENSG00000235303	ENST00000835149.1		n.202+16986A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.360 AC: 54667 AN: 151898 Hom.: 11009 Cov.: 32

Gnomad AFR AF: 0.192

Gnomad AMI AF: 0.478

Gnomad AMR AF: 0.355

Gnomad ASJ AF: 0.335

Gnomad EAS AF: 0.610

Gnomad SAS AF: 0.217

Gnomad FIN AF: 0.466

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.439

Gnomad OTH AF: 0.356

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

GnomAD4 genome AF: 0.360 AC: 54707 AN: 152018 Hom.: 11018 Cov.: 32 AF XY: 0.362 AC XY: 26899 AN XY: 74302

African (AFR) AF: 0.192 AC: 7971 AN: 41494

American (AMR) AF: 0.355 AC: 5424 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.335 AC: 1161 AN: 3470

East Asian (EAS) AF: 0.609 AC: 3148 AN: 5166

South Asian (SAS) AF: 0.219 AC: 1053 AN: 4818

European-Finnish (FIN) AF: 0.466 AC: 4913 AN: 10540

Middle Eastern (MID) AF: 0.150 AC: 44 AN: 294

European-Non Finnish (NFE) AF: 0.439 AC: 29796 AN: 67942

Other (OTH) AF: 0.360 AC: 761 AN: 2114

Alfa AF: 0.407 Hom.: 25541

Bravo AF: 0.352

Asia WGS AF: 0.423 AC: 1466 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	11
DANN	Benign	0.85
PhyloP100		0.42

Splicing

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

Other links and lift over

dbSNP: rs3903239; hg19: chr1-170569317;