rs11597812

Variant names:

• chr10-5263191-C-G
• rs11597812
• ENST00000428920.3:n.512C>G

Variant summary

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

The ENST00000428920.3(ENSG00000231039):​n.512C>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.143 in 152,206 control chromosomes in the GnomAD database, including 2,118 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 0.14 (2117 hom., cov: 32)
  • Exomes 𝑓: 0.20 (1 hom.)
• Consequence: ENSG00000231039 ENST00000428920.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.339
• Publications: 0 publications found

Genes affected

ENSG00000231039 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.273 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000231039	ENST00000428920.3	n.512C>G		non_coding_transcript_exon_variant	Exon 2 of 2	3
ENSG00000231039	ENST00000757036.1	n.390C>G		non_coding_transcript_exon_variant	Exon 3 of 3

Frequencies

GnomAD3 genomes AF: 0.143 AC: 21676 AN: 152058 Hom.: 2112 Cov.: 32

Gnomad AFR AF: 0.277

Gnomad AMI AF: 0.0789

Gnomad AMR AF: 0.0890

Gnomad ASJ AF: 0.146

Gnomad EAS AF: 0.0214

Gnomad SAS AF: 0.0976

Gnomad FIN AF: 0.0599

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.0989

Gnomad OTH AF: 0.141

GnomAD4 exome AF: 0.200 AC: 6 AN: 30 Hom.: 1 Cov.: 0 AF XY: 0.227 AC XY: 5 AN XY: 22

African (AFR) AF: 1.00 AC: 2 AN: 2

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 6

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.200 AC: 4 AN: 20

Other (OTH) AF: 0.00 AC: 0 AN: 2

GnomAD4 genome AF: 0.143 AC: 21708 AN: 152176 Hom.: 2117 Cov.: 32 AF XY: 0.137 AC XY: 10181 AN XY: 74400

African (AFR) AF: 0.277 AC: 11491 AN: 41494

American (AMR) AF: 0.0888 AC: 1357 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.146 AC: 506 AN: 3470

East Asian (EAS) AF: 0.0215 AC: 111 AN: 5174

South Asian (SAS) AF: 0.0973 AC: 469 AN: 4822

European-Finnish (FIN) AF: 0.0599 AC: 636 AN: 10612

Middle Eastern (MID) AF: 0.144 AC: 42 AN: 292

European-Non Finnish (NFE) AF: 0.0989 AC: 6728 AN: 68010

Other (OTH) AF: 0.140 AC: 296 AN: 2112

Alfa AF: 0.125 Hom.: 197

Bravo AF: 0.149

Asia WGS AF: 0.0820 AC: 285 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.2
DANN	Benign	0.49
PhyloP100		-0.34
Mutation Taster		=99/1	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs11597812; hg19: chr10-5305154;