rs7755450

Variant names:

• chr6-67909510-C-T
• rs7755450
• ENST00000653528.1:n.131+20403C>T

Variant summary

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

The ENST00000653528.1(ENSG00000287557):​n.131+20403C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0579 in 152,206 control chromosomes in the GnomAD database, including 413 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 0.058 (413 hom., cov: 32)
• Consequence: ENSG00000287557 ENST00000653528.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.106

Genes affected

ENSG00000287557 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.121 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105377845	XR_942662.1	n.909-11941C>T		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000287557	ENST00000653528.1	n.131+20403C>T		intron_variant	Intron 1 of 3
ENSG00000286680	ENST00000661401.1	n.121-11941C>T		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.0578 AC: 8798 AN: 152088 Hom.: 410 Cov.: 32

Gnomad AFR AF: 0.124

Gnomad AMI AF: 0.0724

Gnomad AMR AF: 0.0292

Gnomad ASJ AF: 0.0216

Gnomad EAS AF: 0.0133

Gnomad SAS AF: 0.0130

Gnomad FIN AF: 0.0263

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.0377

Gnomad OTH AF: 0.0446

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

GnomAD4 genome AF: 0.0579 AC: 8806 AN: 152206 Hom.: 413 Cov.: 32 AF XY: 0.0552 AC XY: 4107 AN XY: 74420

Gnomad4 AFR AF: 0.124

Gnomad4 AMR AF: 0.0292

Gnomad4 ASJ AF: 0.0216

Gnomad4 EAS AF: 0.0135

Gnomad4 SAS AF: 0.0128

Gnomad4 FIN AF: 0.0263

Gnomad4 NFE AF: 0.0377

Gnomad4 OTH AF: 0.0441

Alfa AF: 0.0462 Hom.: 41

Bravo AF: 0.0608

Asia WGS AF: 0.0230 AC: 79 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	3.0
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7755450; hg19: chr6-68619402;