6-164151004-C-T

Variant names:

• chr6-164151004-C-T
• rs4145454
• ENST00000655888.1:n.2346+637C>T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000655888.1(ENSG00000288584):​n.2346+637C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.208 in 152,124 control chromosomes in the GnomAD database, including 3,427 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 0.21 (3427 hom., cov: 32)
• Consequence: ENSG00000288584 ENST00000655888.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.18

Genes affected

ENSG00000288584 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.293 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
ENSG00000288584	ENST00000655888.1	n.2346+637C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.208 AC: 31573 AN: 152006 Hom.: 3432 Cov.: 32

Gnomad AFR AF: 0.145

Gnomad AMI AF: 0.223

Gnomad AMR AF: 0.203

Gnomad ASJ AF: 0.292

Gnomad EAS AF: 0.231

Gnomad SAS AF: 0.306

Gnomad FIN AF: 0.177

Gnomad MID AF: 0.222

Gnomad NFE AF: 0.238

Gnomad OTH AF: 0.226

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

GnomAD4 genome AF: 0.208 AC: 31570 AN: 152124 Hom.: 3427 Cov.: 32 AF XY: 0.205 AC XY: 15220 AN XY: 74348

Gnomad4 AFR AF: 0.145

Gnomad4 AMR AF: 0.202

Gnomad4 ASJ AF: 0.292

Gnomad4 EAS AF: 0.229

Gnomad4 SAS AF: 0.306

Gnomad4 FIN AF: 0.177

Gnomad4 NFE AF: 0.238

Gnomad4 OTH AF: 0.226

Alfa AF: 0.233 Hom.: 2420

Bravo AF: 0.205

Asia WGS AF: 0.272 AC: 948 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.35
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4145454; hg19: chr6-164572036;