5-56727256-T-G

Variant names:

• chr5-56727256-T-G
• rs16886165

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 0.218 in 152,128 control chromosomes in the GnomAD database, including 4,223 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 0.22 (4223 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.911
• Publications: 47 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.341 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: 0.218 AC: 33082 AN: 152010 Hom.: 4208 Cov.: 32

Gnomad AFR AF: 0.333

Gnomad AMI AF: 0.111

Gnomad AMR AF: 0.150

Gnomad ASJ AF: 0.171

Gnomad EAS AF: 0.353

Gnomad SAS AF: 0.335

Gnomad FIN AF: 0.136

Gnomad MID AF: 0.149

Gnomad NFE AF: 0.161

Gnomad OTH AF: 0.202

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

GnomAD4 genome AF: 0.218 AC: 33131 AN: 152128 Hom.: 4223 Cov.: 32 AF XY: 0.219 AC XY: 16299 AN XY: 74392

African (AFR) AF: 0.333 AC: 13817 AN: 41474

American (AMR) AF: 0.150 AC: 2296 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.171 AC: 591 AN: 3466

East Asian (EAS) AF: 0.354 AC: 1824 AN: 5152

South Asian (SAS) AF: 0.335 AC: 1614 AN: 4820

European-Finnish (FIN) AF: 0.136 AC: 1439 AN: 10614

Middle Eastern (MID) AF: 0.156 AC: 46 AN: 294

European-Non Finnish (NFE) AF: 0.161 AC: 10968 AN: 68000

Other (OTH) AF: 0.207 AC: 435 AN: 2106

Alfa AF: 0.179 Hom.: 11170

Bravo AF: 0.222

Asia WGS AF: 0.341 AC: 1182 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	8.0
DANN	Benign	0.83
PhyloP100		0.91

Splicing

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

Other links and lift over

dbSNP: rs16886165; hg19: chr5-56023083; COSMIC: COSV53316951;