chr11-43064544-T-G

Variant names:

• chr11-43064544-T-G
• rs10501293
• ENST00000603543.1:n.541A>C

Variant summary

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

The ENST00000603543.1(ENSG00000271028):​n.541A>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 0.227 in 152,228 control chromosomes in the GnomAD database, including 4,518 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 0.23 (4518 hom., cov: 33)
  • Exomes 𝑓: 0.50 (0 hom.)
• Consequence: ENSG00000271028 ENST00000603543.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.846
• Publications: 9 publications found

Genes affected

ENSG00000271028 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.356 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC100533710		n.43064544T>G		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000271028	ENST00000603543.1	n.541A>C		non_coding_transcript_exon_variant	Exon 2 of 2	6

Frequencies

GnomAD3 genomes AF: 0.227 AC: 34536 AN: 152108 Hom.: 4520 Cov.: 33

Gnomad AFR AF: 0.0997

Gnomad AMI AF: 0.169

Gnomad AMR AF: 0.364

Gnomad ASJ AF: 0.303

Gnomad EAS AF: 0.123

Gnomad SAS AF: 0.260

Gnomad FIN AF: 0.256

Gnomad MID AF: 0.323

Gnomad NFE AF: 0.271

Gnomad OTH AF: 0.245

GnomAD4 exome AF: 0.500 AC: 1 AN: 2 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

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: 0.500 AC: 1 AN: 2

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.227 AC: 34548 AN: 152226 Hom.: 4518 Cov.: 33 AF XY: 0.230 AC XY: 17108 AN XY: 74412

African (AFR) AF: 0.0997 AC: 4146 AN: 41572

American (AMR) AF: 0.364 AC: 5569 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.303 AC: 1051 AN: 3470

East Asian (EAS) AF: 0.123 AC: 639 AN: 5178

South Asian (SAS) AF: 0.260 AC: 1253 AN: 4822

European-Finnish (FIN) AF: 0.256 AC: 2706 AN: 10590

Middle Eastern (MID) AF: 0.310 AC: 91 AN: 294

European-Non Finnish (NFE) AF: 0.271 AC: 18423 AN: 67992

Other (OTH) AF: 0.244 AC: 516 AN: 2112

Alfa AF: 0.257 Hom.: 23438

Bravo AF: 0.228

Asia WGS AF: 0.199 AC: 692 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	1.2
DANN	Benign	0.71
PhyloP100		0.85

Splicing

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

Other links and lift over

dbSNP: rs10501293; hg19: chr11-43086094;