rs7366407

Variant names:

• chr1-115875282-T-A
• rs7366407

Your query was ambiguous. Multiple possible variants found:

• chr1-115875282-T-A
• chr1-115875282-T-C
• chr1-115875282-T-G

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 0.232 in 152,142 control chromosomes in the GnomAD database, including 5,027 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 0.23 (5027 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.446
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.403 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: 0.232 AC: 35333 AN: 152024 Hom.: 5024 Cov.: 32

Gnomad AFR AF: 0.0614

Gnomad AMI AF: 0.349

Gnomad AMR AF: 0.346

Gnomad ASJ AF: 0.324

Gnomad EAS AF: 0.417

Gnomad SAS AF: 0.312

Gnomad FIN AF: 0.271

Gnomad MID AF: 0.399

Gnomad NFE AF: 0.277

Gnomad OTH AF: 0.280

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

GnomAD4 genome AF: 0.232 AC: 35340 AN: 152142 Hom.: 5027 Cov.: 32 AF XY: 0.237 AC XY: 17628 AN XY: 74368

African (AFR) AF: 0.0613 AC: 2549 AN: 41550

American (AMR) AF: 0.345 AC: 5272 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.324 AC: 1126 AN: 3472

East Asian (EAS) AF: 0.418 AC: 2158 AN: 5166

South Asian (SAS) AF: 0.312 AC: 1503 AN: 4818

European-Finnish (FIN) AF: 0.271 AC: 2866 AN: 10580

Middle Eastern (MID) AF: 0.398 AC: 117 AN: 294

European-Non Finnish (NFE) AF: 0.277 AC: 18832 AN: 67974

Other (OTH) AF: 0.283 AC: 599 AN: 2114

Alfa AF: 0.255 Hom.: 706

Bravo AF: 0.233

Asia WGS AF: 0.334 AC: 1158 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	6.4
DANN	Benign	0.76
PhyloP100		0.45

Splicing

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

Other links and lift over

dbSNP: rs7366407; hg19: chr1-116417903; COSMIC: COSV59991031;