rs5009270

Variant names:

• chr7-112519123-G-A
• rs5009270

Your query was ambiguous. Multiple possible variants found:

• chr7-112519123-G-A
• chr7-112519123-G-T

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 0.364 in 151,592 control chromosomes in the GnomAD database, including 10,800 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 0.36 (10800 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0560
• Publications: 10 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.486 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.364 AC: 55170 AN: 151470 Hom.: 10789 Cov.: 31

Gnomad AFR AF: 0.492

Gnomad AMI AF: 0.357

Gnomad AMR AF: 0.288

Gnomad ASJ AF: 0.466

Gnomad EAS AF: 0.0997

Gnomad SAS AF: 0.319

Gnomad FIN AF: 0.373

Gnomad MID AF: 0.551

Gnomad NFE AF: 0.319

Gnomad OTH AF: 0.385

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

GnomAD4 genome AF: 0.364 AC: 55228 AN: 151592 Hom.: 10800 Cov.: 31 AF XY: 0.362 AC XY: 26802 AN XY: 74062

African (AFR) AF: 0.492 AC: 20338 AN: 41352

American (AMR) AF: 0.288 AC: 4379 AN: 15224

Ashkenazi Jewish (ASJ) AF: 0.466 AC: 1615 AN: 3464

East Asian (EAS) AF: 0.0996 AC: 512 AN: 5142

South Asian (SAS) AF: 0.320 AC: 1533 AN: 4796

European-Finnish (FIN) AF: 0.373 AC: 3898 AN: 10462

Middle Eastern (MID) AF: 0.548 AC: 161 AN: 294

European-Non Finnish (NFE) AF: 0.319 AC: 21656 AN: 67846

Other (OTH) AF: 0.386 AC: 811 AN: 2102

Alfa AF: 0.336 Hom.: 12895

Bravo AF: 0.363

Asia WGS AF: 0.238 AC: 827 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.2
DANN	Benign	0.15
PhyloP100		-0.056

Splicing

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

Other links and lift over

dbSNP: rs5009270; hg19: chr7-112159178;