rs1864668

Variant names:

• chr3-197581134-C-A
• rs1864668
• ENST00000453454.6:n.1056-1835G>T

Your query was ambiguous. Multiple possible variants found:

• chr3-197581134-C-A
• chr3-197581134-C-G
• chr3-197581134-C-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000453454.6(ENSG00000291091):​n.1056-1835G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00165 in 151,352 control chromosomes in the GnomAD database, including 6 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 0.0017 (6 hom., cov: 30)
• Consequence: ENSG00000291091 ENST00000453454.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.730
• Publications: 3 publications found

Genes affected

ENSG00000291091 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BS1: Variant frequency is greater than expected in population eas. GnomAd4 allele frequency = 0.00165 (250/151352) while in subpopulation EAS AF = 0.0261 (135/5170). AF 95% confidence interval is 0.0225. There are 6 homozygotes in GnomAd4. There are 136 alleles in the male GnomAd4 subpopulation. Median coverage is 30. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 6 gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000453454.6. 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
	ENSG00000291091	ENST00000453454.6	TSL:4	n.1056-1835G>T		intron	N/A
	ENSG00000291091	ENST00000751206.1		n.1132-1835G>T		intron	N/A
	ENSG00000291091	ENST00000751207.1		n.890-1835G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.00165 AC: 249 AN: 151234 Hom.: 6 Cov.: 30

Gnomad AFR AF: 0.00101

Gnomad AMI AF: 0.0396

Gnomad AMR AF: 0.000197

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.0261

Gnomad SAS AF: 0.00332

Gnomad FIN AF: 0.0000947

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000162

Gnomad OTH AF: 0.00288

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

GnomAD4 genome AF: 0.00165 AC: 250 AN: 151352 Hom.: 6 Cov.: 30 AF XY: 0.00184 AC XY: 136 AN XY: 73984

African (AFR) AF: 0.00100 AC: 41 AN: 40828

American (AMR) AF: 0.000197 AC: 3 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3472

East Asian (EAS) AF: 0.0261 AC: 135 AN: 5170

South Asian (SAS) AF: 0.00353 AC: 17 AN: 4818

European-Finnish (FIN) AF: 0.0000947 AC: 1 AN: 10558

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 292

European-Non Finnish (NFE) AF: 0.000162 AC: 11 AN: 67950

Other (OTH) AF: 0.00285 AC: 6 AN: 2104

Alfa AF: 0.00 Hom.: 653

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.97
DANN	Benign	0.21
PhyloP100		0.73

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: rs1864668;

hg19: chr3-197308005;