rs13223993

Variant names:

• chr7-45911631-G-A
• rs13223993

Your query was ambiguous. Multiple possible variants found:

• chr7-45911631-G-A
• chr7-45911631-G-C

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 0.282 in 152,070 control chromosomes in the GnomAD database, including 7,008 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 0.28 (7008 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.916
• Publications: 18 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 (AFR) allele frequency at 95% confidence interval = 0.438 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: 0.281 AC: 42772 AN: 151952 Hom.: 6983 Cov.: 32

Gnomad AFR AF: 0.443

Gnomad AMI AF: 0.209

Gnomad AMR AF: 0.273

Gnomad ASJ AF: 0.113

Gnomad EAS AF: 0.334

Gnomad SAS AF: 0.157

Gnomad FIN AF: 0.155

Gnomad MID AF: 0.250

Gnomad NFE AF: 0.220

Gnomad OTH AF: 0.271

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

GnomAD4 genome AF: 0.282 AC: 42844 AN: 152070 Hom.: 7008 Cov.: 32 AF XY: 0.277 AC XY: 20579 AN XY: 74326

African (AFR) AF: 0.444 AC: 18393 AN: 41452

American (AMR) AF: 0.273 AC: 4174 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.113 AC: 391 AN: 3470

East Asian (EAS) AF: 0.334 AC: 1730 AN: 5172

South Asian (SAS) AF: 0.157 AC: 754 AN: 4808

European-Finnish (FIN) AF: 0.155 AC: 1642 AN: 10582

Middle Eastern (MID) AF: 0.238 AC: 70 AN: 294

European-Non Finnish (NFE) AF: 0.219 AC: 14922 AN: 67988

Other (OTH) AF: 0.274 AC: 577 AN: 2104

Alfa AF: 0.235 Hom.: 7672

Bravo AF: 0.305

Asia WGS AF: 0.275 AC: 957 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.29
DANN	Benign	0.74
PhyloP100		-0.92

Splicing

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

Other links and lift over

dbSNP: rs13223993; hg19: chr7-45951230;