rs993183

Variant names:

• chr7-46631145-A-G
• rs993183

Your query was ambiguous. Multiple possible variants found:

• chr7-46631145-A-G
• chr7-46631145-A-T

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 0.458 in 151,912 control chromosomes in the GnomAD database, including 16,477 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 0.46 (16477 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.876
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.571 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: 0.458 AC: 69484 AN: 151794 Hom.: 16475 Cov.: 32

Gnomad AFR AF: 0.357

Gnomad AMI AF: 0.546

Gnomad AMR AF: 0.581

Gnomad ASJ AF: 0.509

Gnomad EAS AF: 0.462

Gnomad SAS AF: 0.293

Gnomad FIN AF: 0.393

Gnomad MID AF: 0.522

Gnomad NFE AF: 0.507

Gnomad OTH AF: 0.511

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

GnomAD4 genome AF: 0.458 AC: 69505 AN: 151912 Hom.: 16477 Cov.: 32 AF XY: 0.452 AC XY: 33594 AN XY: 74244

African (AFR) AF: 0.356 AC: 14771 AN: 41434

American (AMR) AF: 0.581 AC: 8878 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.509 AC: 1766 AN: 3470

East Asian (EAS) AF: 0.462 AC: 2387 AN: 5166

South Asian (SAS) AF: 0.293 AC: 1412 AN: 4824

European-Finnish (FIN) AF: 0.393 AC: 4123 AN: 10504

Middle Eastern (MID) AF: 0.524 AC: 153 AN: 292

European-Non Finnish (NFE) AF: 0.507 AC: 34452 AN: 67916

Other (OTH) AF: 0.504 AC: 1066 AN: 2114

Alfa AF: 0.497 Hom.: 77462

Bravo AF: 0.473

Asia WGS AF: 0.359 AC: 1241 AN: 3456

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	4.9
DANN	Benign	0.79
PhyloP100		0.88

Splicing

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

Other links and lift over

dbSNP: rs993183; hg19: chr7-46670743;