rs6660164

Variant names:

• chr1-79983799-G-A
• rs6660164
• ENST00000644002.1:n.460-15929C>T

Variant summary

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

The ENST00000644002.1(ENSG00000285409):​n.460-15929C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.413 in 151,920 control chromosomes in the GnomAD database, including 13,754 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 (13754 hom., cov: 32)
• Consequence: ENSG00000285409 ENST00000644002.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.510
• Publications: 1 publications found

Genes affected

ENSG00000285409 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.475 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
ENSG00000285409	ENST00000644002.1	n.460-15929C>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.413 AC: 62709 AN: 151802 Hom.: 13753 Cov.: 32

Gnomad AFR AF: 0.296

Gnomad AMI AF: 0.291

Gnomad AMR AF: 0.472

Gnomad ASJ AF: 0.545

Gnomad EAS AF: 0.0575

Gnomad SAS AF: 0.380

Gnomad FIN AF: 0.509

Gnomad MID AF: 0.490

Gnomad NFE AF: 0.479

Gnomad OTH AF: 0.432

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

GnomAD4 genome AF: 0.413 AC: 62722 AN: 151920 Hom.: 13754 Cov.: 32 AF XY: 0.413 AC XY: 30690 AN XY: 74268

African (AFR) AF: 0.296 AC: 12267 AN: 41396

American (AMR) AF: 0.472 AC: 7210 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.545 AC: 1890 AN: 3466

East Asian (EAS) AF: 0.0574 AC: 296 AN: 5154

South Asian (SAS) AF: 0.380 AC: 1828 AN: 4814

European-Finnish (FIN) AF: 0.509 AC: 5377 AN: 10556

Middle Eastern (MID) AF: 0.490 AC: 143 AN: 292

European-Non Finnish (NFE) AF: 0.479 AC: 32547 AN: 67944

Other (OTH) AF: 0.426 AC: 899 AN: 2112

Alfa AF: 0.456 Hom.: 4395

Bravo AF: 0.403

Asia WGS AF: 0.219 AC: 763 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.11
DANN	Benign	0.55
PhyloP100		-0.51

Splicing

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

Other links and lift over

dbSNP: rs6660164; hg19: chr1-80449484;