chr4-99398605-T-A

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC102723576	XR_001741777.2	n.387+4228A>T		intron_variant	Intron 3 of 3
LOC102723576	XR_427569.4	n.1284+4228A>T		intron_variant	Intron 3 of 3
LOC102723576	XR_939020.3	n.1284+4228A>T		intron_variant	Intron 3 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000299279	ENST00000762194.1	n.377+4228A>T		intron_variant	Intron 3 of 4
ENSG00000299279	ENST00000762195.1	n.249+4228A>T		intron_variant	Intron 3 of 4
ENSG00000299279	ENST00000762196.1	n.492+4228A>T		intron_variant	Intron 3 of 4
ENSG00000299279	ENST00000762197.1	n.249+4228A>T		intron_variant	Intron 3 of 3

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 v4.3

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

Other links and lift over

dbSNP: rs1583977; hg19: chr4-100319762;