1-1585290-TTTTGTTTG-TTTTG

Variant names:

• chr1-1585290-TTTTG-T
• rs34877486
• ENST00000763257.1:n.247-6814_247-6811delTTTG

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The ENST00000763257.1(ENSG00000299413):​n.247-6814_247-6811delTTTG variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.35 (10191 hom., cov: 0)
• Consequence: ENSG00000299413 ENST00000763257.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.212
• Publications: 1 publications found

Genes affected

ENSG00000299413 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.432 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000763257.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000299413	ENST00000763257.1		n.247-6814_247-6811delTTTG		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.352 AC: 53269 AN: 151358 Hom.: 10187 Cov.: 0

Gnomad AFR AF: 0.205

Gnomad AMI AF: 0.526

Gnomad AMR AF: 0.293

Gnomad ASJ AF: 0.486

Gnomad EAS AF: 0.348

Gnomad SAS AF: 0.269

Gnomad FIN AF: 0.440

Gnomad MID AF: 0.484

Gnomad NFE AF: 0.436

Gnomad OTH AF: 0.391

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

GnomAD4 genome AF: 0.352 AC: 53280 AN: 151476 Hom.: 10191 Cov.: 0 AF XY: 0.350 AC XY: 25882 AN XY: 73984

African (AFR) AF: 0.205 AC: 8464 AN: 41366

American (AMR) AF: 0.293 AC: 4455 AN: 15222

Ashkenazi Jewish (ASJ) AF: 0.486 AC: 1686 AN: 3468

East Asian (EAS) AF: 0.348 AC: 1780 AN: 5118

South Asian (SAS) AF: 0.270 AC: 1296 AN: 4806

European-Finnish (FIN) AF: 0.440 AC: 4601 AN: 10448

Middle Eastern (MID) AF: 0.486 AC: 142 AN: 292

European-Non Finnish (NFE) AF: 0.436 AC: 29568 AN: 67760

Other (OTH) AF: 0.389 AC: 816 AN: 2098

Alfa AF: 0.200 Hom.: 339

Bravo AF: 0.336

Asia WGS AF: 0.291 AC: 1013 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.21

Splicing

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

Other links and lift over

dbSNP: rs34877486; hg19: chr1-1520670;