rs10510338

Positions:

• chr3-6524190-A-G

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

ENSG00000189229 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
LOC105376944	NR_188693.1	n.231+33518A>G		intron_variant
LOC105376944	NR_188694.1	n.231+33518A>G		intron_variant
LOC105376944	NR_188695.1	n.231+33518A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000189229	ENST00000433639.1	n.194+33518A>G		intron_variant		1
ENSG00000189229	ENST00000342990.4	n.145+16233A>G		intron_variant		3
ENSG00000189229	ENST00000414438.2	n.209+33248A>G		intron_variant		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

Gnomad4 AFR AF: 0.138

Gnomad4 AMR AF: 0.0492

Gnomad4 ASJ AF: 0.0199

Gnomad4 EAS AF: 0.0490

Gnomad4 SAS AF: 0.143

Gnomad4 FIN AF: 0.0138

Gnomad4 NFE AF: 0.0140

Gnomad4 OTH AF: 0.0491

Alfa AF: 0.0230 Hom.: 203

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
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10510338; hg19: chr3-6565877;