rs1604355

Variant names:

• chr1-190489877-C-G
• rs1604355
• ENST00000417409.1:n.47-3961C>G

Variant summary

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

The ENST00000417409.1(ENSG00000241505):​n.47-3961C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.158 in 151,912 control chromosomes in the GnomAD database, including 2,051 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 0.16 (2051 hom., cov: 31)
• Consequence: ENSG00000241505 ENST00000417409.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0510
• Publications: 4 publications found

Genes affected

ENSG00000241505 (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 (SAS) allele frequency at 95% confidence interval = 0.207 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000417409.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000241505	ENST00000417409.1	TSL:3	n.47-3961C>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.158 AC: 23998 AN: 151794 Hom.: 2044 Cov.: 31

Gnomad AFR AF: 0.103

Gnomad AMI AF: 0.305

Gnomad AMR AF: 0.150

Gnomad ASJ AF: 0.152

Gnomad EAS AF: 0.216

Gnomad SAS AF: 0.215

Gnomad FIN AF: 0.218

Gnomad MID AF: 0.169

Gnomad NFE AF: 0.175

Gnomad OTH AF: 0.127

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

GnomAD4 genome AF: 0.158 AC: 24011 AN: 151912 Hom.: 2051 Cov.: 31 AF XY: 0.161 AC XY: 11958 AN XY: 74254

African (AFR) AF: 0.103 AC: 4272 AN: 41454

American (AMR) AF: 0.149 AC: 2276 AN: 15226

Ashkenazi Jewish (ASJ) AF: 0.152 AC: 527 AN: 3462

East Asian (EAS) AF: 0.216 AC: 1112 AN: 5152

South Asian (SAS) AF: 0.218 AC: 1050 AN: 4820

European-Finnish (FIN) AF: 0.218 AC: 2301 AN: 10552

Middle Eastern (MID) AF: 0.168 AC: 49 AN: 292

European-Non Finnish (NFE) AF: 0.175 AC: 11882 AN: 67934

Other (OTH) AF: 0.126 AC: 266 AN: 2114

Alfa AF: 0.164 Hom.: 272

Bravo AF: 0.150

Asia WGS AF: 0.190 AC: 661 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.87
DANN	Benign	0.32
PhyloP100		-0.051

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1604355;

hg19: chr1-190459007;