rs6480671

Variant names:

• chr10-73141025-C-T
• rs6480671
• NM_007265.3:c.1128-1288G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 7 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
ECD	NM_007265.3	c.1128-1288G>A		intron_variant	Intron 9 of 13	ENST00000372979.9	NP_009196.1
ECD	NM_001135752.1	c.1226+362G>A		intron_variant	Intron 10 of 14		NP_001129224.1
ECD	NM_001135753.1	c.999-1288G>A		intron_variant	Intron 8 of 12		NP_001129225.1
ECD	NR_024203.1	n.960-1288G>A		intron_variant	Intron 7 of 11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ECD	ENST00000372979.9	c.1128-1288G>A		intron_variant	Intron 9 of 13	1	NM_007265.3	ENSP00000362070.4
ECD	ENST00000430082.6	c.1226+362G>A		intron_variant	Intron 10 of 14	1		ENSP00000401566.1
ECD	ENST00000454759.6	c.999-1288G>A		intron_variant	Intron 8 of 12	1		ENSP00000395786.1
ECD	ENST00000484976.6	n.*221-1288G>A		intron_variant	Intron 7 of 11	1		ENSP00000433778.1

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

African (AFR) AF: 0.336 AC: 13887 AN: 41384

American (AMR) AF: 0.107 AC: 1629 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.128 AC: 444 AN: 3468

East Asian (EAS) AF: 0.305 AC: 1581 AN: 5182

South Asian (SAS) AF: 0.232 AC: 1118 AN: 4828

European-Finnish (FIN) AF: 0.0424 AC: 444 AN: 10466

Middle Eastern (MID) AF: 0.0793 AC: 23 AN: 290

European-Non Finnish (NFE) AF: 0.0652 AC: 4434 AN: 67992

Other (OTH) AF: 0.129 AC: 271 AN: 2106

Alfa AF: 0.131 Hom.: 354

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
PhyloP100		-0.025
Mutation Taster		=100/0	polymorphism (auto)

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: rs6480671; hg19: chr10-74900783;