chr5-73104363-T-C

Variant names:

• chr5-73104363-T-C
• rs683633

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 0.244 in 152,036 control chromosomes in the GnomAD database, including 6,279 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 0.24 (6279 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.396
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.472 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: 0.243 AC: 36967 AN: 151918 Hom.: 6257 Cov.: 32

Gnomad AFR AF: 0.478

Gnomad AMI AF: 0.101

Gnomad AMR AF: 0.187

Gnomad ASJ AF: 0.208

Gnomad EAS AF: 0.208

Gnomad SAS AF: 0.232

Gnomad FIN AF: 0.135

Gnomad MID AF: 0.177

Gnomad NFE AF: 0.139

Gnomad OTH AF: 0.218

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

GnomAD4 genome AF: 0.244 AC: 37030 AN: 152036 Hom.: 6279 Cov.: 32 AF XY: 0.242 AC XY: 17981 AN XY: 74322

African (AFR) AF: 0.477 AC: 19790 AN: 41446

American (AMR) AF: 0.187 AC: 2859 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.208 AC: 722 AN: 3468

East Asian (EAS) AF: 0.208 AC: 1074 AN: 5166

South Asian (SAS) AF: 0.232 AC: 1112 AN: 4800

European-Finnish (FIN) AF: 0.135 AC: 1424 AN: 10586

Middle Eastern (MID) AF: 0.173 AC: 51 AN: 294

European-Non Finnish (NFE) AF: 0.139 AC: 9437 AN: 67972

Other (OTH) AF: 0.222 AC: 469 AN: 2110

Alfa AF: 0.167 Hom.: 4320

Bravo AF: 0.256

Asia WGS AF: 0.262 AC: 915 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.2
DANN	Benign	0.75
PhyloP100		-0.40

Splicing

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

Other links and lift over

dbSNP: rs683633; hg19: chr5-72400190;