rs744307

Variant names:

• chr5-176619566-G-A
• rs744307

Your query was ambiguous. Multiple possible variants found:

• chr5-176619566-G-A
• chr5-176619566-G-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 0.0866 in 152,276 control chromosomes in the GnomAD database, including 1,053 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 0.087 (1053 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.289
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.441 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: 0.0866 AC: 13172 AN: 152158 Hom.: 1042 Cov.: 33

Gnomad AFR AF: 0.0522

Gnomad AMI AF: 0.00440

Gnomad AMR AF: 0.141

Gnomad ASJ AF: 0.0521

Gnomad EAS AF: 0.457

Gnomad SAS AF: 0.153

Gnomad FIN AF: 0.129

Gnomad MID AF: 0.0791

Gnomad NFE AF: 0.0585

Gnomad OTH AF: 0.0947

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

GnomAD4 genome AF: 0.0866 AC: 13192 AN: 152276 Hom.: 1053 Cov.: 33 AF XY: 0.0939 AC XY: 6995 AN XY: 74458

African (AFR) AF: 0.0522 AC: 2169 AN: 41576

American (AMR) AF: 0.141 AC: 2158 AN: 15308

Ashkenazi Jewish (ASJ) AF: 0.0521 AC: 181 AN: 3472

East Asian (EAS) AF: 0.457 AC: 2357 AN: 5160

South Asian (SAS) AF: 0.153 AC: 741 AN: 4832

European-Finnish (FIN) AF: 0.129 AC: 1369 AN: 10604

Middle Eastern (MID) AF: 0.0748 AC: 22 AN: 294

European-Non Finnish (NFE) AF: 0.0584 AC: 3975 AN: 68008

Other (OTH) AF: 0.102 AC: 216 AN: 2112

Alfa AF: 0.0722 Hom.: 1077

Bravo AF: 0.0888

Asia WGS AF: 0.325 AC: 1126 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	2.0
DANN	Benign	0.68
PhyloP100		-0.29

Splicing

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

Other links and lift over

dbSNP: rs744307; hg19: chr5-176046567;