ENST00000529411.1:c.304-9540G>A

Variant names:

• chr11-57399496-C-T
• rs3741085
• ENST00000529411.1:c.304-9540G>A

Variant summary

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

The ENST00000529411.1(ENSG00000254979):​c.304-9540G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0901 in 446,270 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 0.083 (606 hom., cov: 32)
  • Exomes 𝑓: 0.094 (1512 hom.)
• Consequence: ENSG00000254979 ENST00000529411.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.27
• Publications: 5 publications found

Genes affected

ENSG00000254979 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.108 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
ENSG00000254979	ENST00000529411.1	c.304-9540G>A		intron_variant	Intron 2 of 3	4		ENSP00000431536.1
ENSG00000254979	ENST00000534081.5	n.848G>A		splice_region_variant, non_coding_transcript_exon_variant	Exon 8 of 13	2
ENSG00000254979	ENST00000528835.1	n.*212+8084G>A		intron_variant	Intron 1 of 2	3		ENSP00000431480.1

Frequencies

GnomAD3 genomes AF: 0.0826 AC: 12556 AN: 151968 Hom.: 606 Cov.: 32

Gnomad AFR AF: 0.0461

Gnomad AMI AF: 0.149

Gnomad AMR AF: 0.0920

Gnomad ASJ AF: 0.0723

Gnomad EAS AF: 0.0485

Gnomad SAS AF: 0.0739

Gnomad FIN AF: 0.0574

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.110

Gnomad OTH AF: 0.0886

GnomAD2 exomes AF: 0.0880 AC: 11566 AN: 131372 AF XY: 0.0877

Gnomad AFR exome AF: 0.0452

Gnomad AMR exome AF: 0.0891

Gnomad ASJ exome AF: 0.0662

Gnomad EAS exome AF: 0.0387

Gnomad FIN exome AF: 0.0724

Gnomad NFE exome AF: 0.113

Gnomad OTH exome AF: 0.0999

GnomAD4 exome AF: 0.0939 AC: 27630 AN: 294184 Hom.: 1512 Cov.: 0 AF XY: 0.0917 AC XY: 15406 AN XY: 168004

African (AFR) AF: 0.0465 AC: 391 AN: 8408

American (AMR) AF: 0.0897 AC: 2385 AN: 26600

Ashkenazi Jewish (ASJ) AF: 0.0653 AC: 690 AN: 10570

East Asian (EAS) AF: 0.0379 AC: 335 AN: 8846

South Asian (SAS) AF: 0.0742 AC: 4268 AN: 57532

European-Finnish (FIN) AF: 0.0690 AC: 848 AN: 12294

Middle Eastern (MID) AF: 0.0371 AC: 102 AN: 2750

European-Non Finnish (NFE) AF: 0.113 AC: 17286 AN: 153478

Other (OTH) AF: 0.0967 AC: 1325 AN: 13706

GnomAD4 genome AF: 0.0826 AC: 12558 AN: 152086 Hom.: 606 Cov.: 32 AF XY: 0.0799 AC XY: 5939 AN XY: 74350

African (AFR) AF: 0.0460 AC: 1908 AN: 41468

American (AMR) AF: 0.0917 AC: 1400 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.0723 AC: 251 AN: 3472

East Asian (EAS) AF: 0.0490 AC: 254 AN: 5186

South Asian (SAS) AF: 0.0741 AC: 356 AN: 4802

European-Finnish (FIN) AF: 0.0574 AC: 607 AN: 10582

Middle Eastern (MID) AF: 0.0272 AC: 8 AN: 294

European-Non Finnish (NFE) AF: 0.110 AC: 7453 AN: 67998

Other (OTH) AF: 0.0877 AC: 185 AN: 2110

Alfa AF: 0.102 Hom.: 549

Bravo AF: 0.0838

Asia WGS AF: 0.0780 AC: 272 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.26
DANN	Benign	0.83
PhyloP100		-3.3

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs3741085; hg19: chr11-57166969;