ENST00000663591.1:n.399-42291C>A

Variant names:

• chr6-155954557-G-T
• rs4870405
• ENST00000663591.1:n.399-42291C>A

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000663591.1(ENSG00000287092):​n.399-42291C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.403 in 419,724 control chromosomes in the GnomAD database, including 35,078 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 0.41 (13144 hom., cov: 32)
  • Exomes 𝑓: 0.40 (21934 hom.)
• Consequence: ENSG00000287092 ENST00000663591.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.00
• Publications: 6 publications found

Genes affected

ENSG00000287092 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.23).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.581 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000663591.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000287092	ENST00000663591.1		n.399-42291C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.412 AC: 62518 AN: 151862 Hom.: 13123 Cov.: 32

Gnomad AFR AF: 0.378

Gnomad AMI AF: 0.429

Gnomad AMR AF: 0.474

Gnomad ASJ AF: 0.363

Gnomad EAS AF: 0.597

Gnomad SAS AF: 0.395

Gnomad FIN AF: 0.421

Gnomad MID AF: 0.373

Gnomad NFE AF: 0.406

Gnomad OTH AF: 0.420

GnomAD2 exomes AF: 0.405 AC: 44913 AN: 110970 AF XY: 0.399

Gnomad AFR exome AF: 0.353

Gnomad AMR exome AF: 0.482

Gnomad ASJ exome AF: 0.327

Gnomad EAS exome AF: 0.569

Gnomad FIN exome AF: 0.383

Gnomad NFE exome AF: 0.383

Gnomad OTH exome AF: 0.393

GnomAD4 exome AF: 0.398 AC: 106560 AN: 267740 Hom.: 21934 Cov.: 0 AF XY: 0.397 AC XY: 61344 AN XY: 154712

African (AFR) AF: 0.353 AC: 2370 AN: 6718

American (AMR) AF: 0.489 AC: 9054 AN: 18514

Ashkenazi Jewish (ASJ) AF: 0.331 AC: 2995 AN: 9052

East Asian (EAS) AF: 0.587 AC: 5066 AN: 8636

South Asian (SAS) AF: 0.379 AC: 20157 AN: 53130

European-Finnish (FIN) AF: 0.401 AC: 4547 AN: 11348

Middle Eastern (MID) AF: 0.390 AC: 1009 AN: 2584

European-Non Finnish (NFE) AF: 0.388 AC: 56348 AN: 145236

Other (OTH) AF: 0.400 AC: 5014 AN: 12522

GnomAD4 genome AF: 0.412 AC: 62587 AN: 151984 Hom.: 13144 Cov.: 32 AF XY: 0.413 AC XY: 30712 AN XY: 74286

African (AFR) AF: 0.378 AC: 15662 AN: 41432

American (AMR) AF: 0.475 AC: 7254 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.363 AC: 1256 AN: 3464

East Asian (EAS) AF: 0.598 AC: 3095 AN: 5172

South Asian (SAS) AF: 0.395 AC: 1902 AN: 4820

European-Finnish (FIN) AF: 0.421 AC: 4434 AN: 10534

Middle Eastern (MID) AF: 0.371 AC: 109 AN: 294

European-Non Finnish (NFE) AF: 0.406 AC: 27594 AN: 67978

Other (OTH) AF: 0.422 AC: 891 AN: 2112

Alfa AF: 0.404 Hom.: 3050

Bravo AF: 0.422

Asia WGS AF: 0.462 AC: 1606 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.23
CADD	Benign	21
DANN	Benign	0.69
PhyloP100		3.0

Splicing

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

Other links and lift over

dbSNP: rs4870405; hg19: chr6-156275691; COSMIC: COSV67685408;