11-18070118-T-A

Variant names:

• chr11-18070118-T-A
• rs951624
• ENST00000532403.1:n.213A>T

Variant summary

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

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SAAL1	ENST00000532403.1	n.213A>T		non_coding_transcript_exon_variant	Exon 4 of 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

⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.

African (AFR) AF: 0.500 AC: 1 AN: 2

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 2

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 2

Other (OTH) AC: 0 AN: 0

⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

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

African (AFR) AF: 0.0976 AC: 4045 AN: 41438

American (AMR) AF: 0.0973 AC: 1486 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.0511 AC: 177 AN: 3462

East Asian (EAS) AF: 0.0812 AC: 419 AN: 5160

South Asian (SAS) AF: 0.0775 AC: 372 AN: 4800

European-Finnish (FIN) AF: 0.0258 AC: 273 AN: 10570

Middle Eastern (MID) AF: 0.143 AC: 42 AN: 294

European-Non Finnish (NFE) AF: 0.0692 AC: 4700 AN: 67962

Other (OTH) AF: 0.0837 AC: 177 AN: 2114

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
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs951624; hg19: chr11-18091665;