rs10510338

Variant names:

• chr3-6524190-A-G
• rs10510338
• ENST00000433639.1:n.194+33518A>G

Variant summary

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

The ENST00000433639.1(ENSG00000189229):​n.194+33518A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0573 in 152,258 control chromosomes in the GnomAD database, including 490 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 0.057 (490 hom., cov: 33)
• Consequence: ENSG00000189229 ENST00000433639.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.126
• Publications: 2 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=-0.86).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.135 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105376944	NR_188693.1	n.231+33518A>G		intron_variant	Intron 1 of 5
LOC105376944	NR_188694.1	n.231+33518A>G		intron_variant	Intron 1 of 5
LOC105376944	NR_188695.1	n.231+33518A>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+33518A>G		intron_variant	Intron 1 of 4	1
ENSG00000189229	ENST00000342990.4	n.145+16233A>G		intron_variant	Intron 1 of 5	3
ENSG00000189229	ENST00000414438.2	n.209+33248A>G		intron_variant	Intron 1 of 2	3

Frequencies

GnomAD3 genomes AF: 0.0572 AC: 8695 AN: 152140 Hom.: 484 Cov.: 33

Gnomad AFR AF: 0.138

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0493

Gnomad ASJ AF: 0.0199

Gnomad EAS AF: 0.0492

Gnomad SAS AF: 0.142

Gnomad FIN AF: 0.0138

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.0140

Gnomad OTH AF: 0.0478

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

GnomAD4 genome AF: 0.0573 AC: 8717 AN: 152258 Hom.: 490 Cov.: 33 AF XY: 0.0581 AC XY: 4327 AN XY: 74452

African (AFR) AF: 0.138 AC: 5743 AN: 41532

American (AMR) AF: 0.0492 AC: 753 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0199 AC: 69 AN: 3472

East Asian (EAS) AF: 0.0490 AC: 254 AN: 5188

South Asian (SAS) AF: 0.143 AC: 688 AN: 4826

European-Finnish (FIN) AF: 0.0138 AC: 146 AN: 10604

Middle Eastern (MID) AF: 0.0374 AC: 11 AN: 294

European-Non Finnish (NFE) AF: 0.0140 AC: 949 AN: 68018

Other (OTH) AF: 0.0491 AC: 104 AN: 2116

Alfa AF: 0.0284 Hom.: 701

Bravo AF: 0.0598

Asia WGS AF: 0.156 AC: 540 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.49
DANN	Benign	0.59
PhyloP100		-0.13
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs10510338; hg19: chr3-6565877;