7-1180369-C-T

Variant names:

• chr7-1180369-C-T
• rs17234336

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 0.0552 in 152,170 control chromosomes in the GnomAD database, including 239 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 0.055 (239 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.96
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0676 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.0551 AC: 8382 AN: 152052 Hom.: 237 Cov.: 32

Gnomad AFR AF: 0.0695

Gnomad AMI AF: 0.0274

Gnomad AMR AF: 0.0330

Gnomad ASJ AF: 0.0473

Gnomad EAS AF: 0.00289

Gnomad SAS AF: 0.0247

Gnomad FIN AF: 0.0557

Gnomad MID AF: 0.0573

Gnomad NFE AF: 0.0585

Gnomad OTH AF: 0.0459

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

GnomAD4 genome AF: 0.0552 AC: 8398 AN: 152170 Hom.: 239 Cov.: 32 AF XY: 0.0546 AC XY: 4060 AN XY: 74404

African (AFR) AF: 0.0697 AC: 2892 AN: 41502

American (AMR) AF: 0.0329 AC: 503 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.0473 AC: 164 AN: 3470

East Asian (EAS) AF: 0.00289 AC: 15 AN: 5186

South Asian (SAS) AF: 0.0253 AC: 122 AN: 4820

European-Finnish (FIN) AF: 0.0557 AC: 590 AN: 10592

Middle Eastern (MID) AF: 0.0582 AC: 17 AN: 292

European-Non Finnish (NFE) AF: 0.0584 AC: 3974 AN: 68008

Other (OTH) AF: 0.0455 AC: 96 AN: 2112

Alfa AF: 0.0536 Hom.: 357

Bravo AF: 0.0540

Asia WGS AF: 0.0140 AC: 51 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	0.26
DANN	Benign	0.65
PhyloP100		-2.0

Splicing

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

Other links and lift over

dbSNP: rs17234336; hg19: chr7-1220005;