rs10838192

Variant names:

• chr11-43875107-T-C
• rs10838192
• ENST00000528765.1:n.92-178A>G

Variant summary

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

The ENST00000528765.1(ENSG00000246250):​n.92-178A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.207 in 152,146 control chromosomes in the GnomAD database, including 3,537 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 0.21 (3537 hom., cov: 32)
• Consequence: ENSG00000246250 ENST00000528765.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.202
• Publications: 3 publications found

Genes affected

ENSG00000246250 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.352 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105376644	XR_001748200.2	n.151-178A>G		intron_variant	Intron 2 of 2
LOC105376644	XR_931227.3	n.248-178A>G		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000246250	ENST00000528765.1	n.92-178A>G		intron_variant	Intron 1 of 1	3
ENSG00000246250	ENST00000530450.1	n.247+2876A>G		intron_variant	Intron 2 of 3	4
ENSG00000246250	ENST00000720674.1	n.132+2876A>G		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.207 AC: 31414 AN: 152028 Hom.: 3535 Cov.: 32

Gnomad AFR AF: 0.137

Gnomad AMI AF: 0.168

Gnomad AMR AF: 0.213

Gnomad ASJ AF: 0.272

Gnomad EAS AF: 0.232

Gnomad SAS AF: 0.367

Gnomad FIN AF: 0.251

Gnomad MID AF: 0.150

Gnomad NFE AF: 0.225

Gnomad OTH AF: 0.210

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

GnomAD4 genome AF: 0.207 AC: 31443 AN: 152146 Hom.: 3537 Cov.: 32 AF XY: 0.210 AC XY: 15603 AN XY: 74372

African (AFR) AF: 0.137 AC: 5680 AN: 41530

American (AMR) AF: 0.214 AC: 3268 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.272 AC: 945 AN: 3472

East Asian (EAS) AF: 0.232 AC: 1201 AN: 5166

South Asian (SAS) AF: 0.367 AC: 1766 AN: 4818

European-Finnish (FIN) AF: 0.251 AC: 2655 AN: 10572

Middle Eastern (MID) AF: 0.140 AC: 41 AN: 292

European-Non Finnish (NFE) AF: 0.225 AC: 15290 AN: 67984

Other (OTH) AF: 0.210 AC: 444 AN: 2112

Alfa AF: 0.224 Hom.: 2197

Bravo AF: 0.197

Asia WGS AF: 0.277 AC: 964 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	4.9
DANN	Benign	0.50
PhyloP100		0.20

Splicing

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

Other links and lift over

dbSNP: rs10838192; hg19: chr11-43896657;