rs1544457

Variant names:

• chr7-77789973-G-T
• rs1544457

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 0.558 in 152,004 control chromosomes in the GnomAD database, including 25,416 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 0.56 (25416 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.430

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 = 0.779 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: 0.558 AC: 84716 AN: 151884 Hom.: 25359 Cov.: 32

Gnomad AFR AF: 0.786

Gnomad AMI AF: 0.588

Gnomad AMR AF: 0.493

Gnomad ASJ AF: 0.582

Gnomad EAS AF: 0.320

Gnomad SAS AF: 0.557

Gnomad FIN AF: 0.380

Gnomad MID AF: 0.547

Gnomad NFE AF: 0.478

Gnomad OTH AF: 0.556

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

GnomAD4 genome AF: 0.558 AC: 84836 AN: 152004 Hom.: 25416 Cov.: 32 AF XY: 0.552 AC XY: 40964 AN XY: 74276

Gnomad4 AFR AF: 0.786

Gnomad4 AMR AF: 0.492

Gnomad4 ASJ AF: 0.582

Gnomad4 EAS AF: 0.321

Gnomad4 SAS AF: 0.557

Gnomad4 FIN AF: 0.380

Gnomad4 NFE AF: 0.478

Gnomad4 OTH AF: 0.559

Alfa AF: 0.523 Hom.: 3514

Bravo AF: 0.572

Asia WGS AF: 0.538 AC: 1870 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	0.62
DANN	Benign	0.23

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1544457; hg19: chr7-77419290;