rs155206

Variant names:

• chr3-6520644-A-G
• rs155206
• ENST00000433639.1:n.194+29972A>G

Your query was ambiguous. Multiple possible variants found:

• chr3-6520644-A-G
• chr3-6520644-A-T

Variant summary

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

The ENST00000433639.1(ENSG00000189229):​n.194+29972A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.16 in 152,190 control chromosomes in the GnomAD database, including 2,126 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 (2126 hom., cov: 32)
• Consequence: ENSG00000189229 ENST00000433639.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0130
• Publications: 1 publications found

Genes affected

ENSG00000189229 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.3 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105376944	NR_188693.1	n.231+29972A>G		intron_variant	Intron 1 of 5
LOC105376944	NR_188694.1	n.231+29972A>G		intron_variant	Intron 1 of 5
LOC105376944	NR_188695.1	n.231+29972A>G		intron_variant	Intron 1 of 7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000189229	ENST00000433639.1	n.194+29972A>G		intron_variant	Intron 1 of 4	1
ENSG00000189229	ENST00000342990.4	n.145+12687A>G		intron_variant	Intron 1 of 5	3
ENSG00000189229	ENST00000414438.2	n.209+29702A>G		intron_variant	Intron 1 of 2	3

Frequencies

GnomAD3 genomes AF: 0.160 AC: 24381 AN: 152070 Hom.: 2127 Cov.: 32

Gnomad AFR AF: 0.172

Gnomad AMI AF: 0.230

Gnomad AMR AF: 0.134

Gnomad ASJ AF: 0.232

Gnomad EAS AF: 0.312

Gnomad SAS AF: 0.234

Gnomad FIN AF: 0.126

Gnomad MID AF: 0.323

Gnomad NFE AF: 0.142

Gnomad OTH AF: 0.159

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

GnomAD4 genome AF: 0.160 AC: 24382 AN: 152190 Hom.: 2126 Cov.: 32 AF XY: 0.161 AC XY: 11980 AN XY: 74414

African (AFR) AF: 0.172 AC: 7136 AN: 41514

American (AMR) AF: 0.134 AC: 2043 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.232 AC: 804 AN: 3470

East Asian (EAS) AF: 0.312 AC: 1611 AN: 5158

South Asian (SAS) AF: 0.234 AC: 1131 AN: 4824

European-Finnish (FIN) AF: 0.126 AC: 1340 AN: 10606

Middle Eastern (MID) AF: 0.323 AC: 95 AN: 294

European-Non Finnish (NFE) AF: 0.142 AC: 9681 AN: 68008

Other (OTH) AF: 0.157 AC: 331 AN: 2112

Alfa AF: 0.155 Hom.: 560

Bravo AF: 0.162

Asia WGS AF: 0.242 AC: 846 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.4
DANN	Benign	0.58
PhyloP100		-0.013

Splicing

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

Other links and lift over

dbSNP: rs155206; hg19: chr3-6562331;