rs7321904

Variant names:

• chr13-81209054-C-T
• rs7321904

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 0.126 in 152,140 control chromosomes in the GnomAD database, including 1,493 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 0.13 (1493 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.80

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.284 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: 0.126 AC: 19126 AN: 152022 Hom.: 1489 Cov.: 32

Gnomad AFR AF: 0.192

Gnomad AMI AF: 0.0132

Gnomad AMR AF: 0.109

Gnomad ASJ AF: 0.110

Gnomad EAS AF: 0.296

Gnomad SAS AF: 0.153

Gnomad FIN AF: 0.0913

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.0815

Gnomad OTH AF: 0.136

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

GnomAD4 genome AF: 0.126 AC: 19165 AN: 152140 Hom.: 1493 Cov.: 32 AF XY: 0.128 AC XY: 9511 AN XY: 74394

Gnomad4 AFR AF: 0.192

Gnomad4 AMR AF: 0.109

Gnomad4 ASJ AF: 0.110

Gnomad4 EAS AF: 0.297

Gnomad4 SAS AF: 0.154

Gnomad4 FIN AF: 0.0913

Gnomad4 NFE AF: 0.0816

Gnomad4 OTH AF: 0.141

Alfa AF: 0.0941 Hom.: 1045

Bravo AF: 0.129

Asia WGS AF: 0.243 AC: 844 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.071
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7321904; hg19: chr13-81783189; COSMIC: COSV69017272;