rs951624

chr11-18070118-T-Achr11-18070118-T-G

Variant summary

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

The ENST00000532403.1(SAAL1):n.213A>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0772 in 151,982 control chromosomes in the GnomAD database, including 515 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 0.077 (515 hom., cov: 32)
  • Exomes 𝑓: 0.17 (0 hom.)
• Consequence: SAAL1 ENST00000532403.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.14

Genes affected

SAAL1 (HGNC:25158): (serum amyloid A like 1) Acts upstream of or within positive regulation of synoviocyte proliferation. Located in nucleoplasm. [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=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0951 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SAAL1	ENST00000532403.1	n.213A>T		non_coding_transcript_exon_variant	4/4	5

Frequencies

GnomAD3 genomes AF: 0.0772 AC: 11723 AN: 151858 Hom.: 515 Cov.: 32

Gnomad AFR AF: 0.0976

Gnomad AMI AF: 0.0484

Gnomad AMR AF: 0.0974

Gnomad ASJ AF: 0.0511

Gnomad EAS AF: 0.0812

Gnomad SAS AF: 0.0776

Gnomad FIN AF: 0.0258

Gnomad MID AF: 0.142

Gnomad NFE AF: 0.0691

Gnomad OTH AF: 0.0832

GnomAD4 exome AF: 0.167 AC: 1 AN: 6 Hom.: 0 Cov.: 0 AF XY: 0.250 AC XY: 1 AN XY: 4

Gnomad4 AFR exome AF: 0.500

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00

GnomAD4 genome AF: 0.0772 AC: 11735 AN: 151976 Hom.: 515 Cov.: 32 AF XY: 0.0741 AC XY: 5501 AN XY: 74274

Gnomad4 AFR AF: 0.0976

Gnomad4 AMR AF: 0.0973

Gnomad4 ASJ AF: 0.0511

Gnomad4 EAS AF: 0.0812

Gnomad4 SAS AF: 0.0775

Gnomad4 FIN AF: 0.0258

Gnomad4 NFE AF: 0.0692

Gnomad4 OTH AF: 0.0837

Alfa AF: 0.0653 Hom.: 43

Bravo AF: 0.0832

Asia WGS AF: 0.0900 AC: 314 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	1.7
Dann	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs951624; hg19: chr11-18091665;