rs3839019

Variant names:

• chr1-223108950-TGAAGAAAAC-T
• rs3839019
• ENST00000762835.1:n.72_80delAAGAAAACG

Variant summary

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

The ENST00000762835.1(ENSG00000299361):​n.72_80delAAGAAAACG variant causes a non coding transcript exon 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 0.34 (9813 hom., cov: 0)
• Consequence: ENSG00000299361 ENST00000762835.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.35
• Publications: 0 publications found

Genes affected

ENSG00000299361 (HGNC:):

ACMG classification

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

• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.425 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000762835.1. 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
	ENSG00000299361	ENST00000762835.1		n.72_80delAAGAAAACG		non_coding_transcript_exon	Exon 1 of 3
	ENSG00000299361	ENST00000762836.1		n.173_181delAAGAAAACG		non_coding_transcript_exon	Exon 1 of 3
	ENSG00000299361	ENST00000762837.1		n.173_181delAAGAAAACG		non_coding_transcript_exon	Exon 1 of 2

Frequencies

GnomAD3 genomes AF: 0.335 AC: 50845 AN: 151558 Hom.: 9810 Cov.: 0

Gnomad AFR AF: 0.144

Gnomad AMI AF: 0.496

Gnomad AMR AF: 0.323

Gnomad ASJ AF: 0.401

Gnomad EAS AF: 0.208

Gnomad SAS AF: 0.421

Gnomad FIN AF: 0.493

Gnomad MID AF: 0.382

Gnomad NFE AF: 0.429

Gnomad OTH AF: 0.333

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

GnomAD4 genome AF: 0.335 AC: 50874 AN: 151674 Hom.: 9813 Cov.: 0 AF XY: 0.338 AC XY: 25059 AN XY: 74102

African (AFR) AF: 0.144 AC: 5971 AN: 41450

American (AMR) AF: 0.323 AC: 4921 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.401 AC: 1391 AN: 3468

East Asian (EAS) AF: 0.208 AC: 1069 AN: 5144

South Asian (SAS) AF: 0.422 AC: 2018 AN: 4782

European-Finnish (FIN) AF: 0.493 AC: 5186 AN: 10526

Middle Eastern (MID) AF: 0.380 AC: 111 AN: 292

European-Non Finnish (NFE) AF: 0.429 AC: 29061 AN: 67764

Other (OTH) AF: 0.333 AC: 700 AN: 2100

Alfa AF: 0.389 Hom.: 1497

Bravo AF: 0.311

Asia WGS AF: 0.301 AC: 1046 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		1.4

Splicing

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

Other links and lift over

dbSNP: rs3839019; hg19: chr1-223282292;