rs604222

Variant names:

• chr3-193865921-G-A
• rs604222
• ENST00000804626.1:n.114-13304C>T

Your query was ambiguous. Multiple possible variants found:

• chr3-193865921-G-A
• chr3-193865921-G-C
• chr3-193865921-G-T

Variant summary

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

The ENST00000804626.1(ENSG00000304564):​n.114-13304C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.181 in 152,060 control chromosomes in the GnomAD database, including 2,567 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 0.18 (2567 hom., cov: 33)
• Consequence: ENSG00000304564 ENST00000804626.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0780
• Publications: 5 publications found

Genes affected

ENSG00000304564 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.254 is higher than 0.05.

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
ENSG00000304564	ENST00000804626.1	n.114-13304C>T		intron_variant	Intron 1 of 2
ENSG00000304564	ENST00000804627.1	n.429+7539C>T		intron_variant	Intron 2 of 3
ENSG00000304564	ENST00000804628.1	n.510+7539C>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.181 AC: 27440 AN: 151942 Hom.: 2554 Cov.: 33

Gnomad AFR AF: 0.175

Gnomad AMI AF: 0.0822

Gnomad AMR AF: 0.189

Gnomad ASJ AF: 0.173

Gnomad EAS AF: 0.153

Gnomad SAS AF: 0.266

Gnomad FIN AF: 0.148

Gnomad MID AF: 0.237

Gnomad NFE AF: 0.184

Gnomad OTH AF: 0.205

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

GnomAD4 genome AF: 0.181 AC: 27486 AN: 152060 Hom.: 2567 Cov.: 33 AF XY: 0.180 AC XY: 13356 AN XY: 74340

African (AFR) AF: 0.175 AC: 7269 AN: 41456

American (AMR) AF: 0.189 AC: 2888 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.173 AC: 601 AN: 3472

East Asian (EAS) AF: 0.153 AC: 789 AN: 5172

South Asian (SAS) AF: 0.267 AC: 1283 AN: 4814

European-Finnish (FIN) AF: 0.148 AC: 1561 AN: 10558

Middle Eastern (MID) AF: 0.238 AC: 70 AN: 294

European-Non Finnish (NFE) AF: 0.184 AC: 12511 AN: 68002

Other (OTH) AF: 0.208 AC: 439 AN: 2112

Alfa AF: 0.184 Hom.: 8990

Bravo AF: 0.182

Asia WGS AF: 0.222 AC: 775 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.3
DANN	Benign	0.35
PhyloP100		0.078

Splicing

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

Other links and lift over

dbSNP: rs604222; hg19: chr3-193583710;