NM_030971.6:c.771+71C>T

Variant names:

• chr10-101037502-C-T
• rs2275382
• NM_030971.6:c.771+71C>T

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The NM_030971.6(SFXN3):​c.771+71C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.262 in 1,613,064 control chromosomes in the GnomAD database, including 58,954 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 0.20 (3835 hom., cov: 32)
  • Exomes 𝑓: 0.27 (55119 hom.)
• Consequence: SFXN3 NM_030971.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.38
• Publications: 7 publications found

Genes affected

SFXN3 (HGNC:16087): (sideroflexin 3) Enables serine transmembrane transporter activity. Involved in serine import into mitochondrion. Located in mitochondrion. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.279 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SFXN3	NM_030971.6	c.771+71C>T		intron_variant	Intron 9 of 11	ENST00000393459.6	NP_112233.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SFXN3	ENST00000393459.6	c.771+71C>T		intron_variant	Intron 9 of 11	5	NM_030971.6	ENSP00000377103.1

Frequencies

GnomAD3 genomes AF: 0.199 AC: 30228 AN: 152058 Hom.: 3836 Cov.: 32

Gnomad AFR AF: 0.0491

Gnomad AMI AF: 0.297

Gnomad AMR AF: 0.177

Gnomad ASJ AF: 0.348

Gnomad EAS AF: 0.167

Gnomad SAS AF: 0.248

Gnomad FIN AF: 0.210

Gnomad MID AF: 0.287

Gnomad NFE AF: 0.282

Gnomad OTH AF: 0.217

GnomAD4 exome AF: 0.269 AC: 392788 AN: 1460888 Hom.: 55119 Cov.: 36 AF XY: 0.270 AC XY: 196004 AN XY: 726740

African (AFR) AF: 0.0401 AC: 1343 AN: 33470

American (AMR) AF: 0.131 AC: 5863 AN: 44698

Ashkenazi Jewish (ASJ) AF: 0.366 AC: 9545 AN: 26114

East Asian (EAS) AF: 0.130 AC: 5175 AN: 39698

South Asian (SAS) AF: 0.249 AC: 21443 AN: 86212

European-Finnish (FIN) AF: 0.212 AC: 11286 AN: 53244

Middle Eastern (MID) AF: 0.241 AC: 1320 AN: 5476

European-Non Finnish (NFE) AF: 0.289 AC: 321041 AN: 1111658

Other (OTH) AF: 0.261 AC: 15772 AN: 60318

GnomAD4 genome AF: 0.199 AC: 30215 AN: 152176 Hom.: 3835 Cov.: 32 AF XY: 0.195 AC XY: 14536 AN XY: 74414

African (AFR) AF: 0.0489 AC: 2033 AN: 41544

American (AMR) AF: 0.177 AC: 2710 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.348 AC: 1209 AN: 3472

East Asian (EAS) AF: 0.167 AC: 866 AN: 5178

South Asian (SAS) AF: 0.248 AC: 1193 AN: 4820

European-Finnish (FIN) AF: 0.210 AC: 2224 AN: 10586

Middle Eastern (MID) AF: 0.271 AC: 79 AN: 292

European-Non Finnish (NFE) AF: 0.282 AC: 19177 AN: 67960

Other (OTH) AF: 0.215 AC: 454 AN: 2110

Alfa AF: 0.243 Hom.: 2051

Bravo AF: 0.188

Asia WGS AF: 0.181 AC: 628 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	11
DANN	Benign	0.46
PhyloP100		-1.4
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.22		Details are displayed if max score is > 0.2
DS_AG_spliceai		0.22		Position offset: 6

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

Other links and lift over

dbSNP: rs2275382; hg19: chr10-102797259; COSMIC: COSV56520480; COSMIC: COSV56520480;