chr1-52645089-A-C

Position:

• chr1-52645089-A-C

Variant summary

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

The NM_001042693.3(SHISAL2A):​c.322+2087A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.348 in 151,802 control chromosomes in the GnomAD database, including 9,346 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 0.35 (9346 hom., cov: 31)
• Consequence: SHISAL2A NM_001042693.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.311

Genes affected

SHISAL2A (HGNC:28757): (shisa like 2A) 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=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.392 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SHISAL2A	NM_001042693.3	c.322+2087A>C		intron_variant		ENST00000517870.2	NP_001036158.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SHISAL2A	ENST00000517870.2	c.322+2087A>C		intron_variant		1	NM_001042693.3	ENSP00000429726	P1
SHISAL2A	ENST00000401050.7	n.515+2087A>C		intron_variant, non_coding_transcript_variant		1
SHISAL2A	ENST00000424164.1	n.223+2087A>C		intron_variant, non_coding_transcript_variant		2
SHISAL2A	ENST00000440303.5	n.472+2087A>C		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.348 AC: 52810 AN: 151684 Hom.: 9346 Cov.: 31

Gnomad AFR AF: 0.274

Gnomad AMI AF: 0.291

Gnomad AMR AF: 0.316

Gnomad ASJ AF: 0.397

Gnomad EAS AF: 0.378

Gnomad SAS AF: 0.390

Gnomad FIN AF: 0.329

Gnomad MID AF: 0.434

Gnomad NFE AF: 0.396

Gnomad OTH AF: 0.358

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

GnomAD4 genome AF: 0.348 AC: 52842 AN: 151802 Hom.: 9346 Cov.: 31 AF XY: 0.345 AC XY: 25614 AN XY: 74188

Gnomad4 AFR AF: 0.274

Gnomad4 AMR AF: 0.316

Gnomad4 ASJ AF: 0.397

Gnomad4 EAS AF: 0.379

Gnomad4 SAS AF: 0.391

Gnomad4 FIN AF: 0.329

Gnomad4 NFE AF: 0.396

Gnomad4 OTH AF: 0.358

Alfa AF: 0.233 Hom.: 549

Bravo AF: 0.343

Asia WGS AF: 0.343 AC: 1191 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	7.8
DANN	Benign	0.76

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: rs6588434; hg19: chr1-53110761; COSMIC: COSV68979530;