rs13247600

Variant names:

• chr7-121310856-G-C
• rs13247600

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 0.048 in 152,212 control chromosomes in the GnomAD database, including 239 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 0.048 (239 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.162
• Publications: 7 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 = 0.0639 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: 0.0481 AC: 7312 AN: 152094 Hom.: 239 Cov.: 32

Gnomad AFR AF: 0.0119

Gnomad AMI AF: 0.0373

Gnomad AMR AF: 0.0363

Gnomad ASJ AF: 0.0662

Gnomad EAS AF: 0.000192

Gnomad SAS AF: 0.0369

Gnomad FIN AF: 0.120

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.0655

Gnomad OTH AF: 0.0406

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

GnomAD4 genome AF: 0.0480 AC: 7307 AN: 152212 Hom.: 239 Cov.: 32 AF XY: 0.0509 AC XY: 3784 AN XY: 74402

African (AFR) AF: 0.0119 AC: 493 AN: 41536

American (AMR) AF: 0.0363 AC: 555 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.0662 AC: 230 AN: 3472

East Asian (EAS) AF: 0.000193 AC: 1 AN: 5184

South Asian (SAS) AF: 0.0367 AC: 177 AN: 4826

European-Finnish (FIN) AF: 0.120 AC: 1270 AN: 10578

Middle Eastern (MID) AF: 0.0374 AC: 11 AN: 294

European-Non Finnish (NFE) AF: 0.0655 AC: 4452 AN: 67994

Other (OTH) AF: 0.0397 AC: 84 AN: 2114

Alfa AF: 0.0505 Hom.: 28

Bravo AF: 0.0410

Asia WGS AF: 0.0140 AC: 50 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.7
DANN	Benign	0.71
PhyloP100		-0.16

Splicing

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

Other links and lift over

dbSNP: rs13247600; hg19: chr7-120950910;