rs1583977

Variant names:

• chr4-99398605-T-A
• rs1583977
• ENST00000762194.1:n.377+4228A>T

Variant summary

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

The ENST00000762194.1(ENSG00000299279):​n.377+4228A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.125 in 151,998 control chromosomes in the GnomAD database, including 1,205 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 0.12 (1205 hom., cov: 33)
• Consequence: ENSG00000299279 ENST00000762194.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.207
• Publications: 4 publications found

Genes affected

ENSG00000299279 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.133 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000762194.1. 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
	ENSG00000299279	ENST00000762194.1		n.377+4228A>T		intron	N/A
	ENSG00000299279	ENST00000762195.1		n.249+4228A>T		intron	N/A
	ENSG00000299279	ENST00000762196.1		n.492+4228A>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.124 AC: 18904 AN: 151882 Hom.: 1198 Cov.: 33

Gnomad AFR AF: 0.120

Gnomad AMI AF: 0.0548

Gnomad AMR AF: 0.127

Gnomad ASJ AF: 0.0456

Gnomad EAS AF: 0.142

Gnomad SAS AF: 0.101

Gnomad FIN AF: 0.158

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.127

Gnomad OTH AF: 0.112

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

GnomAD4 genome AF: 0.125 AC: 18940 AN: 151998 Hom.: 1205 Cov.: 33 AF XY: 0.127 AC XY: 9400 AN XY: 74308

African (AFR) AF: 0.120 AC: 4997 AN: 41482

American (AMR) AF: 0.128 AC: 1943 AN: 15238

Ashkenazi Jewish (ASJ) AF: 0.0456 AC: 158 AN: 3468

East Asian (EAS) AF: 0.142 AC: 732 AN: 5166

South Asian (SAS) AF: 0.101 AC: 487 AN: 4824

European-Finnish (FIN) AF: 0.158 AC: 1673 AN: 10568

Middle Eastern (MID) AF: 0.0748 AC: 22 AN: 294

European-Non Finnish (NFE) AF: 0.127 AC: 8637 AN: 67938

Other (OTH) AF: 0.114 AC: 241 AN: 2108

Alfa AF: 0.127 Hom.: 162

Bravo AF: 0.122

Asia WGS AF: 0.130 AC: 452 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	2.6
DANN	Benign	0.69
PhyloP100		0.21

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1583977;

hg19: chr4-100319762;