7-155065074-A-T

Position:

• chr7-155065074-A-T

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 0.49 in 151,964 control chromosomes in the GnomAD database, including 20,573 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 0.49 (20573 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.114

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.631 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: 0.490 AC: 74383 AN: 151844 Hom.: 20573 Cov.: 32

Gnomad AFR AF: 0.231

Gnomad AMI AF: 0.588

Gnomad AMR AF: 0.549

Gnomad ASJ AF: 0.625

Gnomad EAS AF: 0.244

Gnomad SAS AF: 0.518

Gnomad FIN AF: 0.522

Gnomad MID AF: 0.586

Gnomad NFE AF: 0.636

Gnomad OTH AF: 0.513

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

GnomAD4 genome AF: 0.490 AC: 74393 AN: 151964 Hom.: 20573 Cov.: 32 AF XY: 0.484 AC XY: 35947 AN XY: 74280

Gnomad4 AFR AF: 0.231

Gnomad4 AMR AF: 0.549

Gnomad4 ASJ AF: 0.625

Gnomad4 EAS AF: 0.243

Gnomad4 SAS AF: 0.519

Gnomad4 FIN AF: 0.522

Gnomad4 NFE AF: 0.636

Gnomad4 OTH AF: 0.509

Alfa AF: 0.537 Hom.: 2859

Bravo AF: 0.480

Asia WGS AF: 0.368 AC: 1281 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.81
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2581845; hg19: chr7-154856784;