chr4-158048530-C-A

Variant names:

• chr4-158048530-C-A
• rs7664129
• ENST00000660468.1:n.583-14371G>T

Variant summary

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

The ENST00000660468.1(ENSG00000287226):​n.583-14371G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.911 in 152,220 control chromosomes in the GnomAD database, including 63,379 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 0.91 (63379 hom., cov: 32)
• Consequence: ENSG00000287226 ENST00000660468.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.153
• Publications: 5 publications found

Genes affected

ENSG00000287226 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.952 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
ENSG00000287226	ENST00000660468.1	n.583-14371G>T		intron_variant	Intron 2 of 4
ENSG00000287226	ENST00000809824.1	n.113+10935G>T		intron_variant	Intron 1 of 3
ENSG00000287226	ENST00000809825.1	n.46+10935G>T		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.911 AC: 138585 AN: 152102 Hom.: 63315 Cov.: 32

Gnomad AFR AF: 0.960

Gnomad AMI AF: 0.897

Gnomad AMR AF: 0.917

Gnomad ASJ AF: 0.831

Gnomad EAS AF: 0.966

Gnomad SAS AF: 0.968

Gnomad FIN AF: 0.867

Gnomad MID AF: 0.918

Gnomad NFE AF: 0.883

Gnomad OTH AF: 0.911

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

GnomAD4 genome AF: 0.911 AC: 138708 AN: 152220 Hom.: 63379 Cov.: 32 AF XY: 0.911 AC XY: 67827 AN XY: 74418

African (AFR) AF: 0.960 AC: 39885 AN: 41542

American (AMR) AF: 0.918 AC: 14027 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.831 AC: 2884 AN: 3472

East Asian (EAS) AF: 0.966 AC: 5008 AN: 5186

South Asian (SAS) AF: 0.968 AC: 4675 AN: 4828

European-Finnish (FIN) AF: 0.867 AC: 9165 AN: 10572

Middle Eastern (MID) AF: 0.918 AC: 270 AN: 294

European-Non Finnish (NFE) AF: 0.883 AC: 60049 AN: 68014

Other (OTH) AF: 0.912 AC: 1927 AN: 2112

Alfa AF: 0.905 Hom.: 10389

Bravo AF: 0.915

Asia WGS AF: 0.957 AC: 3328 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.66
DANN	Benign	0.30
PhyloP100		-0.15

Splicing

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

Other links and lift over

dbSNP: rs7664129; hg19: chr4-158969682;