22-39445695-T-C

Variant names:

• chr22-39445695-T-C
• rs5757676

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 0.855 in 152,252 control chromosomes in the GnomAD database, including 56,139 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 0.86 (56139 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.207
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.976 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: 0.855 AC: 130064 AN: 152134 Hom.: 56072 Cov.: 32

Gnomad AFR AF: 0.962

Gnomad AMI AF: 0.743

Gnomad AMR AF: 0.863

Gnomad ASJ AF: 0.764

Gnomad EAS AF: 0.998

Gnomad SAS AF: 0.886

Gnomad FIN AF: 0.805

Gnomad MID AF: 0.726

Gnomad NFE AF: 0.790

Gnomad OTH AF: 0.826

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

GnomAD4 genome AF: 0.855 AC: 130189 AN: 152252 Hom.: 56139 Cov.: 32 AF XY: 0.855 AC XY: 63644 AN XY: 74428

African (AFR) AF: 0.963 AC: 40010 AN: 41564

American (AMR) AF: 0.863 AC: 13212 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.764 AC: 2652 AN: 3470

East Asian (EAS) AF: 0.998 AC: 5157 AN: 5166

South Asian (SAS) AF: 0.885 AC: 4275 AN: 4828

European-Finnish (FIN) AF: 0.805 AC: 8536 AN: 10606

Middle Eastern (MID) AF: 0.719 AC: 210 AN: 292

European-Non Finnish (NFE) AF: 0.790 AC: 53709 AN: 67994

Other (OTH) AF: 0.828 AC: 1752 AN: 2116

Alfa AF: 0.856 Hom.: 31161

Bravo AF: 0.864

Asia WGS AF: 0.950 AC: 3304 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.8
DANN	Benign	0.65
PhyloP100		-0.21

Splicing

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

Other links and lift over

dbSNP: rs5757676; hg19: chr22-39841700;