rs7290560

Positions:

• chr22-44309360-G-A

Variant summary

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

The NM_001099294.2(SHISAL1):​c.-33+3391C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.171 in 152,110 control chromosomes in the GnomAD database, including 3,261 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 0.17 (3261 hom., cov: 33)
• Consequence: SHISAL1 NM_001099294.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.235

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=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.34 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SHISAL1	NM_001099294.2	c.-33+3391C>T		intron_variant		ENST00000381176.5
SHISAL1	XM_005261790.4	c.-32-8383C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SHISAL1	ENST00000381176.5	c.-33+3391C>T		intron_variant		5	NM_001099294.2	P1

Frequencies

GnomAD3 genomes AF: 0.171 AC: 25992 AN: 151992 Hom.: 3256 Cov.: 33

Gnomad AFR AF: 0.345

Gnomad AMI AF: 0.0824

Gnomad AMR AF: 0.150

Gnomad ASJ AF: 0.0842

Gnomad EAS AF: 0.267

Gnomad SAS AF: 0.125

Gnomad FIN AF: 0.143

Gnomad MID AF: 0.133

Gnomad NFE AF: 0.0770

Gnomad OTH AF: 0.144

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

GnomAD4 genome AF: 0.171 AC: 26030 AN: 152110 Hom.: 3261 Cov.: 33 AF XY: 0.172 AC XY: 12822 AN XY: 74354

Gnomad4 AFR AF: 0.345

Gnomad4 AMR AF: 0.150

Gnomad4 ASJ AF: 0.0842

Gnomad4 EAS AF: 0.266

Gnomad4 SAS AF: 0.126

Gnomad4 FIN AF: 0.143

Gnomad4 NFE AF: 0.0770

Gnomad4 OTH AF: 0.144

Alfa AF: 0.111 Hom.: 595

Bravo AF: 0.179

Asia WGS AF: 0.204 AC: 708 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	4.2
DANN	Benign	0.81

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: rs7290560; hg19: chr22-44705240;