rs1474526

Variant names:

• chr10-122446128-C-T
• rs1474526
• ENST00000811549.1:n.33C>T

Variant summary

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

The ENST00000811549.1(ENSG00000305527):​n.33C>T 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 0.062 in 152,150 control chromosomes in the GnomAD database, including 422 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 0.062 (422 hom., cov: 32)
• Consequence: ENSG00000305527 ENST00000811549.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.947
• Publications: 5 publications found

Genes affected

ENSG00000305527 (HGNC:):

ENSG00000285955 (HGNC:58122):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.09 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
ENSG00000305527	ENST00000811549.1	n.33C>T		non_coding_transcript_exon_variant	Exon 1 of 2
ENSG00000285955	ENST00000650300.1	n.1853-9496G>A		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.0620 AC: 9428 AN: 152032 Hom.: 423 Cov.: 32

Gnomad AFR AF: 0.0150

Gnomad AMI AF: 0.0504

Gnomad AMR AF: 0.0522

Gnomad ASJ AF: 0.0709

Gnomad EAS AF: 0.000385

Gnomad SAS AF: 0.0174

Gnomad FIN AF: 0.118

Gnomad MID AF: 0.00949

Gnomad NFE AF: 0.0920

Gnomad OTH AF: 0.0602

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

GnomAD4 genome AF: 0.0620 AC: 9427 AN: 152150 Hom.: 422 Cov.: 32 AF XY: 0.0613 AC XY: 4559 AN XY: 74382

African (AFR) AF: 0.0150 AC: 621 AN: 41518

American (AMR) AF: 0.0521 AC: 797 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0709 AC: 246 AN: 3472

East Asian (EAS) AF: 0.000386 AC: 2 AN: 5178

South Asian (SAS) AF: 0.0176 AC: 85 AN: 4824

European-Finnish (FIN) AF: 0.118 AC: 1251 AN: 10578

Middle Eastern (MID) AF: 0.0102 AC: 3 AN: 294

European-Non Finnish (NFE) AF: 0.0920 AC: 6250 AN: 67970

Other (OTH) AF: 0.0596 AC: 126 AN: 2114

Alfa AF: 0.0761 Hom.: 363

Bravo AF: 0.0536

Asia WGS AF: 0.00953 AC: 34 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.9
DANN	Benign	0.50
PhyloP100		-0.95

Splicing

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

Other links and lift over

dbSNP: rs1474526; hg19: chr10-124205644;