rs848413

Variant names:

• chr7-108870756-C-G
• rs848413

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 0.157 in 144,112 control chromosomes in the GnomAD database, including 5,780 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 0.16 (5780 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.44
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.534 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: 0.156 AC: 22509 AN: 144056 Hom.: 5761 Cov.: 29

Gnomad AFR AF: 0.539

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0601

Gnomad ASJ AF: 0.0370

Gnomad EAS AF: 0.000204

Gnomad SAS AF: 0.00177

Gnomad FIN AF: 0.000227

Gnomad MID AF: 0.0552

Gnomad NFE AF: 0.00293

Gnomad OTH AF: 0.122

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

GnomAD4 genome AF: 0.157 AC: 22564 AN: 144112 Hom.: 5780 Cov.: 29 AF XY: 0.152 AC XY: 10579 AN XY: 69738

African (AFR) AF: 0.540 AC: 21121 AN: 39124

American (AMR) AF: 0.0599 AC: 861 AN: 14362

Ashkenazi Jewish (ASJ) AF: 0.0370 AC: 124 AN: 3350

East Asian (EAS) AF: 0.000205 AC: 1 AN: 4886

South Asian (SAS) AF: 0.00155 AC: 7 AN: 4502

European-Finnish (FIN) AF: 0.000227 AC: 2 AN: 8818

Middle Eastern (MID) AF: 0.0597 AC: 16 AN: 268

European-Non Finnish (NFE) AF: 0.00293 AC: 193 AN: 65946

Other (OTH) AF: 0.121 AC: 239 AN: 1974

Alfa AF: 0.105 Hom.: 436

Bravo AF: 0.180

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.68
DANN	Benign	0.55
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs848413; hg19: chr7-108510813;