rs9993819

Variant names:

• chr4-178134462-T-C
• rs9993819

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 0.308 in 152,046 control chromosomes in the GnomAD database, including 7,461 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 0.31 (7461 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.889
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.352 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: 0.308 AC: 46810 AN: 151928 Hom.: 7457 Cov.: 32

Gnomad AFR AF: 0.246

Gnomad AMI AF: 0.285

Gnomad AMR AF: 0.264

Gnomad ASJ AF: 0.327

Gnomad EAS AF: 0.220

Gnomad SAS AF: 0.337

Gnomad FIN AF: 0.344

Gnomad MID AF: 0.263

Gnomad NFE AF: 0.355

Gnomad OTH AF: 0.283

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

GnomAD4 genome AF: 0.308 AC: 46837 AN: 152046 Hom.: 7461 Cov.: 32 AF XY: 0.307 AC XY: 22829 AN XY: 74296

African (AFR) AF: 0.246 AC: 10200 AN: 41494

American (AMR) AF: 0.264 AC: 4028 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.327 AC: 1133 AN: 3470

East Asian (EAS) AF: 0.220 AC: 1136 AN: 5160

South Asian (SAS) AF: 0.338 AC: 1628 AN: 4820

European-Finnish (FIN) AF: 0.344 AC: 3640 AN: 10574

Middle Eastern (MID) AF: 0.259 AC: 76 AN: 294

European-Non Finnish (NFE) AF: 0.355 AC: 24144 AN: 67928

Other (OTH) AF: 0.281 AC: 592 AN: 2110

Alfa AF: 0.335 Hom.: 27160

Bravo AF: 0.299

Asia WGS AF: 0.258 AC: 896 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	0.13
DANN	Benign	0.59
PhyloP100		-0.89

Splicing

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

Other links and lift over

dbSNP: rs9993819; hg19: chr4-179055616;