rs7704225

chr5-144148409-G-A

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 0.153 in 152,142 control chromosomes in the GnomAD database, including 1,944 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 0.15 (1944 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.265

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.242 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.153 AC: 23257 AN: 152024 Hom.: 1941 Cov.: 32

Gnomad AFR AF: 0.125

Gnomad AMI AF: 0.0954

Gnomad AMR AF: 0.248

Gnomad ASJ AF: 0.201

Gnomad EAS AF: 0.0281

Gnomad SAS AF: 0.160

Gnomad FIN AF: 0.101

Gnomad MID AF: 0.212

Gnomad NFE AF: 0.164

Gnomad OTH AF: 0.172

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

GnomAD4 genome AF: 0.153 AC: 23263 AN: 152142 Hom.: 1944 Cov.: 32 AF XY: 0.153 AC XY: 11377 AN XY: 74370

Gnomad4 AFR AF: 0.125

Gnomad4 AMR AF: 0.249

Gnomad4 ASJ AF: 0.201

Gnomad4 EAS AF: 0.0278

Gnomad4 SAS AF: 0.159

Gnomad4 FIN AF: 0.101

Gnomad4 NFE AF: 0.164

Gnomad4 OTH AF: 0.170

Alfa AF: 0.169 Hom.: 4668

Bravo AF: 0.164

Asia WGS AF: 0.0900 AC: 315 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	1.2
Dann	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7704225; hg19: chr5-143527974;