22-44312775-T-C

Variant names:

• chr22-44312775-T-C
• rs7510924
• NM_001099294.2:c.-57A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

Genes affected

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

ENSG00000298486 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001099294.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SHISAL1	NM_001099294.2	MANE Select	c.-57A>G		5_prime_UTR	Exon 1 of 5	NP_001092764.1	Q3SXP7

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SHISAL1	ENST00000381176.5	TSL:5 MANE Select	c.-57A>G		5_prime_UTR	Exon 1 of 5	ENSP00000370568.4	Q3SXP7
	ENSG00000298486	ENST00000755912.1		n.-161T>C		upstream_gene	N/A
	ENSG00000298486	ENST00000755913.1		n.-202T>C		upstream_gene	N/A

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

African (AFR) AF: 0.667 AC: 4 AN: 6

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AF: 1.00 AC: 2 AN: 2

East Asian (EAS) AF: 1.00 AC: 2 AN: 2

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.833 AC: 5 AN: 6

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.946 AC: 87 AN: 92

Other (OTH) AF: 0.917 AC: 11 AN: 12

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

African (AFR) AF: 0.804 AC: 33429 AN: 41558

American (AMR) AF: 0.866 AC: 13240 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.917 AC: 3183 AN: 3472

East Asian (EAS) AF: 0.926 AC: 4798 AN: 5184

South Asian (SAS) AF: 0.883 AC: 4263 AN: 4828

European-Finnish (FIN) AF: 0.855 AC: 9067 AN: 10610

Middle Eastern (MID) AF: 0.864 AC: 254 AN: 294

European-Non Finnish (NFE) AF: 0.912 AC: 62032 AN: 68016

Other (OTH) AF: 0.885 AC: 1872 AN: 2116

Alfa AF: 0.899 Hom.: 77095

Bravo AF: 0.872

Asia WGS AF: 0.890 AC: 3095 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	3.7
DANN	Benign	0.33
PhyloP100		-0.16
PromoterAI		-0.011	Neutral

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

Other links and lift over

dbSNP: rs7510924; hg19: chr22-44708655;