rs1544459

Positions:

• chr7-77788267-T-C

Variant summary

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

The variant allele was found at a frequency of 0.544 in 151,968 control chromosomes in the GnomAD database, including 24,556 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 0.54 (24556 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.259

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.79 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.544 AC: 82575 AN: 151850 Hom.: 24500 Cov.: 31

Gnomad AFR AF: 0.797

Gnomad AMI AF: 0.585

Gnomad AMR AF: 0.464

Gnomad ASJ AF: 0.553

Gnomad EAS AF: 0.319

Gnomad SAS AF: 0.543

Gnomad FIN AF: 0.368

Gnomad MID AF: 0.475

Gnomad NFE AF: 0.452

Gnomad OTH AF: 0.529

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

GnomAD4 genome AF: 0.544 AC: 82697 AN: 151968 Hom.: 24556 Cov.: 31 AF XY: 0.538 AC XY: 39959 AN XY: 74250

Gnomad4 AFR AF: 0.797

Gnomad4 AMR AF: 0.463

Gnomad4 ASJ AF: 0.553

Gnomad4 EAS AF: 0.320

Gnomad4 SAS AF: 0.543

Gnomad4 FIN AF: 0.368

Gnomad4 NFE AF: 0.452

Gnomad4 OTH AF: 0.532

Alfa AF: 0.504 Hom.: 3343

Bravo AF: 0.557

Asia WGS AF: 0.528 AC: 1837 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	0.90
DANN	Benign	0.20

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1544459; hg19: chr7-77417584;