rs1544459

Variant names:

• chr7-77788267-T-C
• rs1544459

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 14 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.797 AC: 33054 AN: 41458

American (AMR) AF: 0.463 AC: 7078 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.553 AC: 1919 AN: 3468

East Asian (EAS) AF: 0.320 AC: 1645 AN: 5146

South Asian (SAS) AF: 0.543 AC: 2612 AN: 4810

European-Finnish (FIN) AF: 0.368 AC: 3878 AN: 10542

Middle Eastern (MID) AF: 0.500 AC: 147 AN: 294

European-Non Finnish (NFE) AF: 0.452 AC: 30709 AN: 67950

Other (OTH) AF: 0.532 AC: 1124 AN: 2112

Alfa AF: 0.512 Hom.: 3576

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
PhyloP100		-0.26

Splicing

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

Other links and lift over

dbSNP: rs1544459; hg19: chr7-77417584;