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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000528765.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000246250	ENST00000528765.1	TSL:3	n.92-178A>G		intron	N/A
	ENSG00000246250	ENST00000530450.1	TSL:4	n.247+2876A>G		intron	N/A
	ENSG00000246250	ENST00000720674.1		n.132+2876A>G		intron	N/A

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 v4.9

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;