chr22-44312775-T-C

Position:

• chr22-44312775-T-C

Variant summary

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

The NM_001099294.2(SHISAL1):​c.-57A>G variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.873 in 152,402 control chromosomes in the GnomAD database, including 58,305 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 0.87 (58254 hom., cov: 35)
  • Exomes 𝑓: 0.93 (51 hom.)
• Consequence: SHISAL1 NM_001099294.2 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.163

Genes affected

SHISAL1 (HGNC:29335): (shisa like 1) Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.906 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SHISAL1	NM_001099294.2	c.-57A>G		5_prime_UTR_variant	1/5	ENST00000381176.5	NP_001092764.1
SHISAL1	XM_005261790.4	c.-32-11798A>G		intron_variant			XP_005261847.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SHISAL1	ENST00000381176.5	c.-57A>G		5_prime_UTR_variant	1/5	5	NM_001099294.2	ENSP00000370568	P1

Frequencies

GnomAD3 genomes AF: 0.873 AC: 132856 AN: 152164 Hom.: 58204 Cov.: 35

Gnomad AFR AF: 0.804

Gnomad AMI AF: 0.907

Gnomad AMR AF: 0.866

Gnomad ASJ AF: 0.917

Gnomad EAS AF: 0.925

Gnomad SAS AF: 0.883

Gnomad FIN AF: 0.855

Gnomad MID AF: 0.867

Gnomad NFE AF: 0.912

Gnomad OTH AF: 0.883

GnomAD4 exome AF: 0.925 AC: 111 AN: 120 Hom.: 51 Cov.: 0 AF XY: 0.918 AC XY: 90 AN XY: 98

Gnomad4 AFR exome AF: 0.667

Gnomad4 ASJ exome AF: 1.00

Gnomad4 EAS exome AF: 1.00

Gnomad4 FIN exome AF: 0.833

Gnomad4 NFE exome AF: 0.946

Gnomad4 OTH exome AF: 0.917

GnomAD4 genome AF: 0.873 AC: 132965 AN: 152282 Hom.: 58254 Cov.: 35 AF XY: 0.872 AC XY: 64903 AN XY: 74472

Gnomad4 AFR AF: 0.804

Gnomad4 AMR AF: 0.866

Gnomad4 ASJ AF: 0.917

Gnomad4 EAS AF: 0.926

Gnomad4 SAS AF: 0.883

Gnomad4 FIN AF: 0.855

Gnomad4 NFE AF: 0.912

Gnomad4 OTH AF: 0.885

Alfa AF: 0.904 Hom.: 59482

Bravo AF: 0.872

Asia WGS AF: 0.890 AC: 3095 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	3.7
DANN	Benign	0.33

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs7510924; hg19: chr22-44708655;