rs5756444

Variant names:

• chr22-36982410-T-C
• rs5756444

Your query was ambiguous. Multiple possible variants found:

• chr22-36982410-T-C
• chr22-36982410-T-G

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 0.348 in 152,136 control chromosomes in the GnomAD database, including 9,473 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 0.35 (9473 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0250
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.523 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.349 AC: 52981 AN: 152018 Hom.: 9475 Cov.: 32

Gnomad AFR AF: 0.308

Gnomad AMI AF: 0.384

Gnomad AMR AF: 0.416

Gnomad ASJ AF: 0.416

Gnomad EAS AF: 0.540

Gnomad SAS AF: 0.327

Gnomad FIN AF: 0.299

Gnomad MID AF: 0.335

Gnomad NFE AF: 0.348

Gnomad OTH AF: 0.373

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

GnomAD4 genome AF: 0.348 AC: 53004 AN: 152136 Hom.: 9473 Cov.: 32 AF XY: 0.348 AC XY: 25892 AN XY: 74382

African (AFR) AF: 0.307 AC: 12762 AN: 41504

American (AMR) AF: 0.416 AC: 6355 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.416 AC: 1443 AN: 3468

East Asian (EAS) AF: 0.540 AC: 2786 AN: 5160

South Asian (SAS) AF: 0.327 AC: 1576 AN: 4826

European-Finnish (FIN) AF: 0.299 AC: 3168 AN: 10586

Middle Eastern (MID) AF: 0.327 AC: 96 AN: 294

European-Non Finnish (NFE) AF: 0.348 AC: 23682 AN: 67992

Other (OTH) AF: 0.373 AC: 787 AN: 2110

Alfa AF: 0.357 Hom.: 16824

Bravo AF: 0.360

Asia WGS AF: 0.400 AC: 1389 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	5.3
DANN	Benign	0.62
PhyloP100		-0.025

Splicing

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

Other links and lift over

dbSNP: rs5756444; hg19: chr22-37378451;