chr7-155065074-A-T

Variant names:

• chr7-155065074-A-T
• rs2581845

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	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

African (AFR) AF: 0.231 AC: 9573 AN: 41454

American (AMR) AF: 0.549 AC: 8383 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.625 AC: 2167 AN: 3468

East Asian (EAS) AF: 0.243 AC: 1259 AN: 5174

South Asian (SAS) AF: 0.519 AC: 2493 AN: 4802

European-Finnish (FIN) AF: 0.522 AC: 5512 AN: 10554

Middle Eastern (MID) AF: 0.568 AC: 166 AN: 292

European-Non Finnish (NFE) AF: 0.636 AC: 43231 AN: 67926

Other (OTH) AF: 0.509 AC: 1074 AN: 2112

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.81
DANN	Benign	0.77
PhyloP100		0.11

Splicing

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

Other links and lift over

dbSNP: rs2581845; hg19: chr7-154856784;