rs1657278

chr7-155093114-C-A

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 0.704 in 152,150 control chromosomes in the GnomAD database, including 38,629 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 0.70 (38629 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.26

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.87 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: 0.704 AC: 107028 AN: 152032 Hom.: 38587 Cov.: 33

Gnomad AFR AF: 0.878

Gnomad AMI AF: 0.559

Gnomad AMR AF: 0.675

Gnomad ASJ AF: 0.648

Gnomad EAS AF: 0.614

Gnomad SAS AF: 0.627

Gnomad FIN AF: 0.581

Gnomad MID AF: 0.652

Gnomad NFE AF: 0.642

Gnomad OTH AF: 0.688

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

GnomAD4 genome AF: 0.704 AC: 107118 AN: 152150 Hom.: 38629 Cov.: 33 AF XY: 0.700 AC XY: 52061 AN XY: 74366

Gnomad4 AFR AF: 0.878

Gnomad4 AMR AF: 0.675

Gnomad4 ASJ AF: 0.648

Gnomad4 EAS AF: 0.614

Gnomad4 SAS AF: 0.627

Gnomad4 FIN AF: 0.581

Gnomad4 NFE AF: 0.642

Gnomad4 OTH AF: 0.680

Alfa AF: 0.672 Hom.: 4374

Bravo AF: 0.717

Asia WGS AF: 0.596 AC: 2077 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	0.21
Dann	Benign	0.15

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1657278; hg19: chr7-154884824;