rs1657278

Variant names:

• chr7-155093114-C-A
• rs1657278

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;