11-112960736-A-G

Variant names:

• chr11-112960736-A-G
• rs2301228
• ENST00000500537.3:n.505T>C

Variant summary

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

The ENST00000500537.3(ENSG00000247416):​n.505T>C 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 0.0875 in 152,238 control chromosomes in the GnomAD database, including 1,198 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 0.087 (1198 hom., cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: ENSG00000247416 ENST00000500537.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.35
• Publications: 9 publications found

Genes affected

ENSG00000247416 (HGNC:58155):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.182 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NCAM1-AS2	NR_120563.1	n.477T>C		non_coding_transcript_exon_variant	Exon 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000247416	ENST00000500537.3	n.505T>C		non_coding_transcript_exon_variant	Exon 3 of 3	1
ENSG00000247416	ENST00000532002.2	n.533T>C		non_coding_transcript_exon_variant	Exon 3 of 3	4
ENSG00000247416	ENST00000649843.1	n.479T>C		non_coding_transcript_exon_variant	Exon 3 of 3

Frequencies

GnomAD3 genomes AF: 0.0873 AC: 13285 AN: 152120 Hom.: 1195 Cov.: 32

Gnomad AFR AF: 0.185

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.164

Gnomad ASJ AF: 0.0141

Gnomad EAS AF: 0.138

Gnomad SAS AF: 0.00911

Gnomad FIN AF: 0.172

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.00479

Gnomad OTH AF: 0.0665

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 6 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 4

African (AFR) AC: 0 AN: 0

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) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

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

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.0875 AC: 13314 AN: 152238 Hom.: 1198 Cov.: 32 AF XY: 0.0948 AC XY: 7053 AN XY: 74430

African (AFR) AF: 0.186 AC: 7709 AN: 41518

American (AMR) AF: 0.164 AC: 2511 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0141 AC: 49 AN: 3468

East Asian (EAS) AF: 0.138 AC: 713 AN: 5180

South Asian (SAS) AF: 0.00891 AC: 43 AN: 4824

European-Finnish (FIN) AF: 0.172 AC: 1819 AN: 10600

Middle Eastern (MID) AF: 0.0204 AC: 6 AN: 294

European-Non Finnish (NFE) AF: 0.00479 AC: 326 AN: 68036

Other (OTH) AF: 0.0653 AC: 138 AN: 2112

Alfa AF: 0.0285 Hom.: 1123

Bravo AF: 0.0929

Asia WGS AF: 0.0860 AC: 299 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	6.4
DANN	Benign	0.62
PhyloP100		1.4
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: rs2301228; hg19: chr11-112831459;