5-132813717-C-T

Variant names:

• chr5-132813717-C-T
• rs1228041238
• NM_175873.6:c.96C>T

Variant summary

Our verdict is Likely benign. The variant received -3 ACMG points: 2P and 5B. PM2 BP4_Strong BP7

The NM_175873.6(SOWAHA):​c.96C>T​(p.Asn32Asn) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000719 in 1,391,098 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.

• Frequency:
  • Genomes: not found (cov: 32)
  • Exomes 𝑓: 7.2e-7 (0 hom.)
• Consequence: SOWAHA NM_175873.6 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.622
• Publications: 0 publications found

Genes affected

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

ACMG classification

Our verdict: Likely_benign. The variant received -3 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.47).
• BP7: Synonymous conserved (PhyloP=0.622 with no splicing effect.

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.96C>T	p.Asn32Asn	synonymous	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.96C>T	p.Asn32Asn	synonymous	Exon 1 of 1	ENSP00000367965.2	Q2M3V2

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 7.19e-7 AC: 1 AN: 1391098 Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0 AN XY: 685930

African (AFR) AF: 0.00 AC: 0 AN: 30492

American (AMR) AF: 0.00 AC: 0 AN: 35486

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 24932

East Asian (EAS) AF: 0.00 AC: 0 AN: 35084

South Asian (SAS) AF: 0.00 AC: 0 AN: 78830

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 47588

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 4784

European-Non Finnish (NFE) AF: 9.29e-7 AC: 1 AN: 1076270

Other (OTH) AF: 0.00 AC: 0 AN: 57632

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.47
CADD	Benign	10
DANN	Benign	0.94
PhyloP100		0.62
PromoterAI		0.013	Neutral

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: rs1228041238; hg19: chr5-132149409;