rs6480671

chr10-73141025-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_007265.3(ECD):c.1128-1288G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.158 in 151,902 control chromosomes in the GnomAD database, including 3,136 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 0.16 (3136 hom., cov: 30)
• Consequence: ECD NM_007265.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0250

Genes affected

ECD (HGNC:17029): (ecdysoneless cell cycle regulator) Enables histone acetyltransferase binding activity. Involved in positive regulation of transcription by RNA polymerase II. Located in cytosol and nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.331 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ECD	NM_007265.3	c.1128-1288G>A		intron_variant		ENST00000372979.9
ECD	NM_001135752.1	c.1226+362G>A		intron_variant
ECD	NM_001135753.1	c.999-1288G>A		intron_variant
ECD	NR_024203.1	n.960-1288G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ECD	ENST00000372979.9	c.1128-1288G>A		intron_variant		1	NM_007265.3	P1
ECD	ENST00000430082.6	c.1226+362G>A		intron_variant		1
ECD	ENST00000454759.6	c.999-1288G>A		intron_variant		1
ECD	ENST00000484976.6	c.*221-1288G>A		intron_variant, NMD_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.157 AC: 23853 AN: 151786 Hom.: 3111 Cov.: 30

Gnomad AFR AF: 0.335

Gnomad AMI AF: 0.107

Gnomad AMR AF: 0.107

Gnomad ASJ AF: 0.128

Gnomad EAS AF: 0.305

Gnomad SAS AF: 0.233

Gnomad FIN AF: 0.0424

Gnomad MID AF: 0.0796

Gnomad NFE AF: 0.0652

Gnomad OTH AF: 0.127

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

GnomAD4 genome AF: 0.158 AC: 23929 AN: 151902 Hom.: 3136 Cov.: 30 AF XY: 0.158 AC XY: 11734 AN XY: 74254

Gnomad4 AFR AF: 0.336

Gnomad4 AMR AF: 0.107

Gnomad4 ASJ AF: 0.128

Gnomad4 EAS AF: 0.305

Gnomad4 SAS AF: 0.232

Gnomad4 FIN AF: 0.0424

Gnomad4 NFE AF: 0.0652

Gnomad4 OTH AF: 0.129

Alfa AF: 0.125 Hom.: 315

Bravo AF: 0.168

Asia WGS AF: 0.270 AC: 936 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	6.8
Dann	Benign	0.70

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

Publications

LitVar

Other links and lift over

dbSNP: rs6480671; hg19: chr10-74900783;