rs1320401881

Variant names:

• chr5-132813776-C-G
• rs1320401881
• NM_175873.6:c.155C>G

Your query was ambiguous. Multiple possible variants found:

• chr5-132813776-C-G
• chr5-132813776-C-T

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_175873.6(SOWAHA):​c.155C>G​(p.Ala52Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000716 in 1,395,990 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. A52V) has been classified as Uncertain significance.

• Frequency:
  • Genomes: not found (cov: 32)
  • Exomes 𝑓: 7.2e-7 (0 hom.)
• Consequence: SOWAHA NM_175873.6 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.03
• Publications: 0 publications found

Genes affected

SOWAHA (HGNC:27033): (sosondowah ankyrin repeat domain family member A)

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.23153737).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_175873.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SOWAHA	NM_175873.6	MANE Select	c.155C>G	p.Ala52Gly	missense	Exon 1 of 1	NP_787069.4

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SOWAHA	ENST00000378693.4	TSL:6 MANE Select	c.155C>G	p.Ala52Gly	missense	Exon 1 of 1	ENSP00000367965.2	Q2M3V2

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 7.16e-7 AC: 1 AN: 1395990 Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0 AN XY: 688500

African (AFR) AF: 0.00 AC: 0 AN: 31276

American (AMR) AF: 0.0000281 AC: 1 AN: 35622

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 25096

East Asian (EAS) AF: 0.00 AC: 0 AN: 35606

South Asian (SAS) AF: 0.00 AC: 0 AN: 79156

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 47804

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 5606

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 1077936

Other (OTH) AF: 0.00 AC: 0 AN: 57888

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.18
BayesDel_addAF	Benign	-0.12	T
BayesDel_noAF	Benign	-0.41
CADD	Uncertain	23
DANN	Uncertain	1.0
Eigen	Uncertain	0.23
Eigen_PC	Benign	0.22
FATHMM_MKL	Benign	0.62	D
M_CAP	Uncertain	0.28	D
MetaRNN	Benign	0.23	T
MetaSVM	Benign	-0.85	T
PhyloP100		2.0
PrimateAI	Pathogenic	0.83	D
PROVEAN	Benign	-1.5	N
REVEL	Benign	0.081
Sift	Uncertain	0.0070	D
Sift4G	Benign	0.10	T
Vest4		0.21
MutPred		0.34		Gain of methylation at R51 (P = 0.0601)
MVP		0.22
ClinPred		0.79	D
GERP RS		4.5
PromoterAI		0.0038	Neutral
gMVP		0.23
Mutation Taster		=79/21	polymorphism

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: rs1320401881; hg19: chr5-132149468;