rs7704225

Variant names:

• chr5-144148409-G-A
• rs7704225

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 0.153 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
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.125 AC: 5170 AN: 41522

American (AMR) AF: 0.249 AC: 3797 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.201 AC: 695 AN: 3466

East Asian (EAS) AF: 0.0278 AC: 144 AN: 5188

South Asian (SAS) AF: 0.159 AC: 764 AN: 4818

European-Finnish (FIN) AF: 0.101 AC: 1066 AN: 10592

Middle Eastern (MID) AF: 0.207 AC: 61 AN: 294

European-Non Finnish (NFE) AF: 0.164 AC: 11120 AN: 67968

Other (OTH) AF: 0.170 AC: 359 AN: 2110

Alfa AF: 0.165 Hom.: 9480

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
PhyloP100		-0.27

Splicing

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

Other links and lift over

dbSNP: rs7704225; hg19: chr5-143527974;