rs738415

Positions:

• chr22-49702165-A-G
• chr22-49702165-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.903 in 152,222 control chromosomes in the GnomAD database, including 62,245 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 0.90 (62245 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.154

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.918 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.903 AC: 137416 AN: 152104 Hom.: 62207 Cov.: 33

Gnomad AFR AF: 0.903

Gnomad AMI AF: 0.868

Gnomad AMR AF: 0.930

Gnomad ASJ AF: 0.929

Gnomad EAS AF: 0.729

Gnomad SAS AF: 0.907

Gnomad FIN AF: 0.874

Gnomad MID AF: 0.902

Gnomad NFE AF: 0.914

Gnomad OTH AF: 0.918

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

GnomAD4 genome AF: 0.903 AC: 137511 AN: 152222 Hom.: 62245 Cov.: 33 AF XY: 0.900 AC XY: 67011 AN XY: 74418

Gnomad4 AFR AF: 0.903

Gnomad4 AMR AF: 0.930

Gnomad4 ASJ AF: 0.929

Gnomad4 EAS AF: 0.728

Gnomad4 SAS AF: 0.906

Gnomad4 FIN AF: 0.874

Gnomad4 NFE AF: 0.914

Gnomad4 OTH AF: 0.916

Alfa AF: 0.915 Hom.: 36697

Bravo AF: 0.907

Asia WGS AF: 0.808 AC: 2811 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	4.0
DANN	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs738415; hg19: chr22-50095813;