chr7-155465199-A-G

Variant names:

• chr7-155465199-A-G
• rs1861958

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 0.159 in 152,082 control chromosomes in the GnomAD database, including 2,290 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 0.16 (2290 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.67
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.258 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: 0.159 AC: 24144 AN: 151964 Hom.: 2281 Cov.: 32

Gnomad AFR AF: 0.262

Gnomad AMI AF: 0.0603

Gnomad AMR AF: 0.112

Gnomad ASJ AF: 0.141

Gnomad EAS AF: 0.0977

Gnomad SAS AF: 0.193

Gnomad FIN AF: 0.118

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.118

Gnomad OTH AF: 0.148

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

GnomAD4 genome AF: 0.159 AC: 24190 AN: 152082 Hom.: 2290 Cov.: 32 AF XY: 0.158 AC XY: 11716 AN XY: 74342

African (AFR) AF: 0.262 AC: 10876 AN: 41438

American (AMR) AF: 0.111 AC: 1703 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.141 AC: 489 AN: 3470

East Asian (EAS) AF: 0.0975 AC: 505 AN: 5178

South Asian (SAS) AF: 0.194 AC: 930 AN: 4802

European-Finnish (FIN) AF: 0.118 AC: 1246 AN: 10602

Middle Eastern (MID) AF: 0.143 AC: 42 AN: 294

European-Non Finnish (NFE) AF: 0.118 AC: 8032 AN: 67996

Other (OTH) AF: 0.148 AC: 312 AN: 2114

Alfa AF: 0.125 Hom.: 2331

Bravo AF: 0.162

Asia WGS AF: 0.122 AC: 426 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	7.8
DANN	Benign	0.62
PhyloP100		1.7

Splicing

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

Other links and lift over

dbSNP: rs1861958; hg19: chr7-155257894;