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

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
ENSG00000291091	ENST00000453454.6	n.1056-1835G>T		intron_variant	Intron 9 of 10	4
ENSG00000291091	ENST00000751206.1	n.1132-1835G>T		intron_variant	Intron 8 of 11
ENSG00000291091	ENST00000751207.1	n.890-1835G>T		intron_variant	Intron 7 of 10

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 v4.3

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

Other links and lift over

dbSNP: rs1864668; hg19: chr3-197308005;