chr7-155976055-A-C

Position:

• chr7-155976055-A-C

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 0.905 in 152,164 control chromosomes in the GnomAD database, including 63,044 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 0.91 (63044 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.921

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.977 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.906 AC: 137704 AN: 152046 Hom.: 63025 Cov.: 32

Gnomad AFR AF: 0.758

Gnomad AMI AF: 0.895

Gnomad AMR AF: 0.948

Gnomad ASJ AF: 0.928

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.954

Gnomad FIN AF: 0.973

Gnomad MID AF: 0.889

Gnomad NFE AF: 0.964

Gnomad OTH AF: 0.907

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

GnomAD4 genome AF: 0.905 AC: 137765 AN: 152164 Hom.: 63044 Cov.: 32 AF XY: 0.908 AC XY: 67597 AN XY: 74412

Gnomad4 AFR AF: 0.757

Gnomad4 AMR AF: 0.948

Gnomad4 ASJ AF: 0.928

Gnomad4 EAS AF: 1.00

Gnomad4 SAS AF: 0.954

Gnomad4 FIN AF: 0.973

Gnomad4 NFE AF: 0.964

Gnomad4 OTH AF: 0.908

Alfa AF: 0.935 Hom.: 27096

Bravo AF: 0.896

Asia WGS AF: 0.947 AC: 3290 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.40
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10267337; hg19: chr7-155768749;