rs7732370

Variant names:

• chr5-121695435-G-A
• rs7732370

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 0.337 in 151,756 control chromosomes in the GnomAD database, including 9,459 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 0.34 (9459 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.318
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.412 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: 0.338 AC: 51188 AN: 151636 Hom.: 9458 Cov.: 31

Gnomad AFR AF: 0.206

Gnomad AMI AF: 0.341

Gnomad AMR AF: 0.298

Gnomad ASJ AF: 0.405

Gnomad EAS AF: 0.264

Gnomad SAS AF: 0.304

Gnomad FIN AF: 0.434

Gnomad MID AF: 0.320

Gnomad NFE AF: 0.416

Gnomad OTH AF: 0.342

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

GnomAD4 genome AF: 0.337 AC: 51197 AN: 151756 Hom.: 9459 Cov.: 31 AF XY: 0.335 AC XY: 24862 AN XY: 74164

African (AFR) AF: 0.206 AC: 8514 AN: 41418

American (AMR) AF: 0.298 AC: 4536 AN: 15232

Ashkenazi Jewish (ASJ) AF: 0.405 AC: 1402 AN: 3466

East Asian (EAS) AF: 0.264 AC: 1355 AN: 5124

South Asian (SAS) AF: 0.302 AC: 1454 AN: 4808

European-Finnish (FIN) AF: 0.434 AC: 4569 AN: 10530

Middle Eastern (MID) AF: 0.330 AC: 97 AN: 294

European-Non Finnish (NFE) AF: 0.416 AC: 28239 AN: 67872

Other (OTH) AF: 0.343 AC: 721 AN: 2104

Alfa AF: 0.386 Hom.: 19637

Bravo AF: 0.318

Asia WGS AF: 0.284 AC: 986 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.95
DANN	Benign	0.41
PhyloP100		-0.32

Splicing

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

Other links and lift over

dbSNP: rs7732370; hg19: chr5-121031130;