ENST00000440461.3:n.258+1677A>T

Variant names:

• chr10-102852578-T-A
• rs11191419
• ENST00000440461.3:n.258+1677A>T

Variant summary

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

The ENST00000440461.3(ENSG00000282772):​n.258+1677A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.357 in 151,720 control chromosomes in the GnomAD database, including 9,928 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 0.36 (9928 hom., cov: 30)
• Consequence: ENSG00000282772 ENST00000440461.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.827
• Publications: 61 publications found

Genes affected

ENSG00000282772 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.545 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000440461.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000282772	ENST00000440461.3	TSL:5	n.258+1677A>T		intron	N/A
	ENSG00000282772	ENST00000629474.2	TSL:5	n.260-949A>T		intron	N/A
	ENSG00000282772	ENST00000631443.1	TSL:4	n.260-949A>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.357 AC: 54174 AN: 151600 Hom.: 9920 Cov.: 30

Gnomad AFR AF: 0.348

Gnomad AMI AF: 0.196

Gnomad AMR AF: 0.370

Gnomad ASJ AF: 0.374

Gnomad EAS AF: 0.563

Gnomad SAS AF: 0.319

Gnomad FIN AF: 0.310

Gnomad MID AF: 0.370

Gnomad NFE AF: 0.355

Gnomad OTH AF: 0.368

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

GnomAD4 genome AF: 0.357 AC: 54221 AN: 151720 Hom.: 9928 Cov.: 30 AF XY: 0.356 AC XY: 26408 AN XY: 74166

African (AFR) AF: 0.348 AC: 14418 AN: 41384

American (AMR) AF: 0.370 AC: 5634 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.374 AC: 1296 AN: 3466

East Asian (EAS) AF: 0.562 AC: 2872 AN: 5108

South Asian (SAS) AF: 0.319 AC: 1534 AN: 4802

European-Finnish (FIN) AF: 0.310 AC: 3271 AN: 10548

Middle Eastern (MID) AF: 0.374 AC: 110 AN: 294

European-Non Finnish (NFE) AF: 0.356 AC: 24129 AN: 67870

Other (OTH) AF: 0.370 AC: 778 AN: 2100

Alfa AF: 0.356 Hom.: 1209

Bravo AF: 0.365

Asia WGS AF: 0.391 AC: 1358 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	4.4
DANN	Benign	0.66
PhyloP100		0.83

Splicing

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

Other links and lift over

dbSNP: rs11191419; hg19: chr10-104612335;