7-155057913-C-T

Variant names:

• chr7-155057913-C-T
• rs1440461

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 0.55 in 151,928 control chromosomes in the GnomAD database, including 23,930 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 0.55 (23930 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00700

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.634 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: 0.550 AC: 83525 AN: 151810 Hom.: 23923 Cov.: 31

Gnomad AFR AF: 0.387

Gnomad AMI AF: 0.586

Gnomad AMR AF: 0.622

Gnomad ASJ AF: 0.643

Gnomad EAS AF: 0.413

Gnomad SAS AF: 0.554

Gnomad FIN AF: 0.537

Gnomad MID AF: 0.617

Gnomad NFE AF: 0.639

Gnomad OTH AF: 0.567

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

GnomAD4 genome AF: 0.550 AC: 83544 AN: 151928 Hom.: 23930 Cov.: 31 AF XY: 0.545 AC XY: 40488 AN XY: 74244

Gnomad4 AFR AF: 0.387

Gnomad4 AMR AF: 0.622

Gnomad4 ASJ AF: 0.643

Gnomad4 EAS AF: 0.412

Gnomad4 SAS AF: 0.554

Gnomad4 FIN AF: 0.537

Gnomad4 NFE AF: 0.639

Gnomad4 OTH AF: 0.563

Alfa AF: 0.581 Hom.: 7701

Bravo AF: 0.550

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	2.0
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1440461; hg19: chr7-154849623;