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. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.492

Gnomad4 AMR AF: 0.288

Gnomad4 ASJ AF: 0.466

Gnomad4 EAS AF: 0.0996

Gnomad4 SAS AF: 0.320

Gnomad4 FIN AF: 0.373

Gnomad4 NFE AF: 0.319

Gnomad4 OTH AF: 0.386

Alfa AF: 0.334 Hom.: 10728

Bravo AF: 0.363

Asia WGS AF: 0.238 AC: 827 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5009270; hg19: chr7-112159178;