rs757537

Variant names:

• chr5-132815379-A-G
• rs757537
• NM_175873.6:c.*108A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_175873.6(SOWAHA):​c.*108A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.135 in 1,048,904 control chromosomes in the GnomAD database, including 10,198 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 0.11 (1105 hom., cov: 33)
  • Exomes 𝑓: 0.14 (9093 hom.)
• Consequence: SOWAHA NM_175873.6 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.349
• Publications: 17 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.185 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SOWAHA	NM_175873.6	c.*108A>G		3_prime_UTR_variant	Exon 1 of 1	ENST00000378693.4	NP_787069.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SOWAHA	ENST00000378693.4	c.*108A>G		3_prime_UTR_variant	Exon 1 of 1	6	NM_175873.6	ENSP00000367965.2

Frequencies

GnomAD3 genomes AF: 0.114 AC: 17315 AN: 152084 Hom.: 1104 Cov.: 33

Gnomad AFR AF: 0.0724

Gnomad AMI AF: 0.0516

Gnomad AMR AF: 0.0822

Gnomad ASJ AF: 0.116

Gnomad EAS AF: 0.118

Gnomad SAS AF: 0.194

Gnomad FIN AF: 0.126

Gnomad MID AF: 0.177

Gnomad NFE AF: 0.138

Gnomad OTH AF: 0.125

GnomAD4 exome AF: 0.138 AC: 123887 AN: 896702 Hom.: 9093 Cov.: 12 AF XY: 0.140 AC XY: 62616 AN XY: 446008

African (AFR) AF: 0.0730 AC: 1517 AN: 20780

American (AMR) AF: 0.0760 AC: 1527 AN: 20086

Ashkenazi Jewish (ASJ) AF: 0.113 AC: 1857 AN: 16494

East Asian (EAS) AF: 0.125 AC: 4138 AN: 33018

South Asian (SAS) AF: 0.191 AC: 10338 AN: 54102

European-Finnish (FIN) AF: 0.136 AC: 6065 AN: 44544

Middle Eastern (MID) AF: 0.178 AC: 768 AN: 4312

European-Non Finnish (NFE) AF: 0.139 AC: 92384 AN: 662732

Other (OTH) AF: 0.130 AC: 5293 AN: 40634

GnomAD4 genome AF: 0.114 AC: 17330 AN: 152202 Hom.: 1105 Cov.: 33 AF XY: 0.114 AC XY: 8514 AN XY: 74408

African (AFR) AF: 0.0725 AC: 3009 AN: 41532

American (AMR) AF: 0.0821 AC: 1255 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.116 AC: 404 AN: 3468

East Asian (EAS) AF: 0.119 AC: 613 AN: 5172

South Asian (SAS) AF: 0.195 AC: 941 AN: 4820

European-Finnish (FIN) AF: 0.126 AC: 1332 AN: 10594

Middle Eastern (MID) AF: 0.173 AC: 51 AN: 294

European-Non Finnish (NFE) AF: 0.138 AC: 9416 AN: 68004

Other (OTH) AF: 0.124 AC: 262 AN: 2114

Alfa AF: 0.125 Hom.: 1726

Bravo AF: 0.107

Asia WGS AF: 0.130 AC: 451 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	2.1
DANN	Benign	0.63
PhyloP100		-0.35
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs757537; hg19: chr5-132151071;