rs198039

Variant names:

• chr5-175526740-G-A
• rs198039
• NM_022754.7:c.*6G>A

Your query was ambiguous. Multiple possible variants found:

• chr5-175526740-G-A
• chr5-175526740-G-C

Variant summary

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

The NM_022754.7(SFXN1):​c.*6G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.165 in 1,609,326 control chromosomes in the GnomAD database, including 26,664 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 0.23 (4970 hom., cov: 33)
  • Exomes 𝑓: 0.16 (21694 hom.)
• Consequence: SFXN1 NM_022754.7 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.440

Genes affected

SFXN1 (HGNC:16085): (sideroflexin 1) Enables D-serine transmembrane transporter activity and L-serine transmembrane transporter activity. Involved in D-serine transport; L-serine transport; and serine import into mitochondrion. Located in mitochondrion. Is integral component of mitochondrial inner membrane. [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=-0.8).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.403 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SFXN1	NM_022754.7	c.*6G>A		3_prime_UTR_variant	Exon 11 of 11	ENST00000321442.10	NP_073591.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SFXN1	ENST00000321442.10	c.*6G>A		3_prime_UTR_variant	Exon 11 of 11	1	NM_022754.7	ENSP00000316905.5
SFXN1	ENST00000421887.2	n.408G>A		non_coding_transcript_exon_variant	Exon 4 of 4	4

Frequencies

GnomAD3 genomes AF: 0.225 AC: 34275 AN: 152144 Hom.: 4963 Cov.: 33

Gnomad AFR AF: 0.408

Gnomad AMI AF: 0.137

Gnomad AMR AF: 0.168

Gnomad ASJ AF: 0.198

Gnomad EAS AF: 0.224

Gnomad SAS AF: 0.353

Gnomad FIN AF: 0.116

Gnomad MID AF: 0.206

Gnomad NFE AF: 0.138

Gnomad OTH AF: 0.203

GnomAD3 exomes AF: 0.194 AC: 48784 AN: 251158 Hom.: 5854 AF XY: 0.196 AC XY: 26630 AN XY: 135736

Gnomad AFR exome AF: 0.408

Gnomad AMR exome AF: 0.179

Gnomad ASJ exome AF: 0.195

Gnomad EAS exome AF: 0.231

Gnomad SAS exome AF: 0.339

Gnomad FIN exome AF: 0.123

Gnomad NFE exome AF: 0.138

Gnomad OTH exome AF: 0.175

GnomAD4 exome AF: 0.158 AC: 230441 AN: 1457064 Hom.: 21694 Cov.: 29 AF XY: 0.162 AC XY: 117802 AN XY: 725230

Gnomad4 AFR exome AF: 0.409

Gnomad4 AMR exome AF: 0.177

Gnomad4 ASJ exome AF: 0.197

Gnomad4 EAS exome AF: 0.234

Gnomad4 SAS exome AF: 0.332

Gnomad4 FIN exome AF: 0.120

Gnomad4 NFE exome AF: 0.133

Gnomad4 OTH exome AF: 0.174

GnomAD4 genome AF: 0.225 AC: 34323 AN: 152262 Hom.: 4970 Cov.: 33 AF XY: 0.224 AC XY: 16675 AN XY: 74440

Gnomad4 AFR AF: 0.408

Gnomad4 AMR AF: 0.168

Gnomad4 ASJ AF: 0.198

Gnomad4 EAS AF: 0.223

Gnomad4 SAS AF: 0.354

Gnomad4 FIN AF: 0.116

Gnomad4 NFE AF: 0.138

Gnomad4 OTH AF: 0.205

Alfa AF: 0.161 Hom.: 3014

Bravo AF: 0.234

Asia WGS AF: 0.327 AC: 1136 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	0.51
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		2.1

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

Publications

LitVar

Other links and lift over

dbSNP: rs198039; hg19: chr5-174953743; COSMIC: COSV58492815; COSMIC: COSV58492815;