rs7318913

Variant names:

• chr13-67997905-C-G
• rs7318913

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 0.0411 in 151,956 control chromosomes in the GnomAD database, including 170 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 0.041 (170 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.700
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0623 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: 0.0412 AC: 6249 AN: 151838 Hom.: 171 Cov.: 32

Gnomad AFR AF: 0.0139

Gnomad AMI AF: 0.0495

Gnomad AMR AF: 0.0659

Gnomad ASJ AF: 0.0562

Gnomad EAS AF: 0.000579

Gnomad SAS AF: 0.00912

Gnomad FIN AF: 0.0351

Gnomad MID AF: 0.102

Gnomad NFE AF: 0.0566

Gnomad OTH AF: 0.0654

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

GnomAD4 genome AF: 0.0411 AC: 6247 AN: 151956 Hom.: 170 Cov.: 32 AF XY: 0.0401 AC XY: 2981 AN XY: 74266

African (AFR) AF: 0.0139 AC: 578 AN: 41522

American (AMR) AF: 0.0657 AC: 1001 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.0562 AC: 195 AN: 3470

East Asian (EAS) AF: 0.000580 AC: 3 AN: 5172

South Asian (SAS) AF: 0.00912 AC: 44 AN: 4822

European-Finnish (FIN) AF: 0.0351 AC: 371 AN: 10576

Middle Eastern (MID) AF: 0.110 AC: 32 AN: 292

European-Non Finnish (NFE) AF: 0.0566 AC: 3842 AN: 67846

Other (OTH) AF: 0.0648 AC: 136 AN: 2100

Alfa AF: 0.0439 Hom.: 28

Bravo AF: 0.0429

Asia WGS AF: 0.00665 AC: 23 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.56
DANN	Benign	0.39
PhyloP100		-0.70

Splicing

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

Other links and lift over

dbSNP: rs7318913; hg19: chr13-68572037;