6-164151004-C-T

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 publications found

Genes affected

ENSG00000288584 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000655888.1. 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
	ENSG00000288584	ENST00000655888.1		n.2346+637C>T		intron	N/A
	ENSG00000288696	ENST00000850151.1		n.312-86750C>T		intron	N/A
	ENSG00000288696	ENST00000850152.1		n.372-86750C>T		intron	N/A

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

African (AFR) AF: 0.145 AC: 6015 AN: 41492

American (AMR) AF: 0.202 AC: 3093 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.292 AC: 1013 AN: 3470

East Asian (EAS) AF: 0.229 AC: 1182 AN: 5152

South Asian (SAS) AF: 0.306 AC: 1473 AN: 4818

European-Finnish (FIN) AF: 0.177 AC: 1877 AN: 10600

Middle Eastern (MID) AF: 0.231 AC: 68 AN: 294

European-Non Finnish (NFE) AF: 0.238 AC: 16170 AN: 67984

Other (OTH) AF: 0.226 AC: 476 AN: 2106

Alfa AF: 0.232 Hom.: 3309

Bravo AF: 0.205

Asia WGS AF: 0.272 AC: 948 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.35
DANN	Benign	0.60
PhyloP100		-2.2

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: rs4145454;

hg19: chr6-164572036;