rs7290560

Variant names:

• chr22-44309360-G-A
• rs7290560
• NM_001099294.2:c.-33+3391C>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 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]

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
SHISAL1	NM_001099294.2	c.-33+3391C>T		intron_variant	Intron 1 of 4	ENST00000381176.5	NP_001092764.1
SHISAL1	XM_005261790.4	c.-32-8383C>T		intron_variant	Intron 1 of 4		XP_005261847.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SHISAL1	ENST00000381176.5	c.-33+3391C>T		intron_variant	Intron 1 of 4	5	NM_001099294.2	ENSP00000370568.4

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

African (AFR) AF: 0.345 AC: 14291 AN: 41452

American (AMR) AF: 0.150 AC: 2290 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.0842 AC: 292 AN: 3468

East Asian (EAS) AF: 0.266 AC: 1376 AN: 5164

South Asian (SAS) AF: 0.126 AC: 609 AN: 4820

European-Finnish (FIN) AF: 0.143 AC: 1517 AN: 10602

Middle Eastern (MID) AF: 0.136 AC: 40 AN: 294

European-Non Finnish (NFE) AF: 0.0770 AC: 5237 AN: 67988

Other (OTH) AF: 0.144 AC: 303 AN: 2110

Alfa AF: 0.112 Hom.: 1345

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
PhyloP100		0.23

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: rs7290560; hg19: chr22-44705240;