rs560659

Variant names:

• chr1-100057980-G-A
• rs560659
• NM_033055.3:c.181-686G>A

Variant summary

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

The NM_033055.3(SLC71A1):​c.181-686G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.22 in 152,074 control chromosomes in the GnomAD database, including 5,087 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 0.22 (5087 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: SLC71A1 NM_033055.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.33
• Publications: 4 publications found

Genes affected

SLC71A1 (HGNC:23363): (major facilitator superfamily domain containing 14A) Predicted to enable transmembrane transporter activity. Predicted to be involved in transmembrane transport. Predicted to act upstream of or within acrosome assembly; sperm mitochondrion organization; and spermatid nucleus differentiation. Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

ENSG00000283761 (HGNC:):

ENSG00000241073 (HGNC:58237):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.429 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_033055.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC71A1	NM_033055.3	MANE Select	c.181-686G>A		intron	N/A	NP_149044.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MFSD14A	ENST00000370152.8	TSL:1 MANE Select	c.181-686G>A		intron	N/A	ENSP00000359171.3
	ENSG00000283761	ENST00000639037.1	TSL:5	c.850-686G>A		intron	N/A	ENSP00000492745.1
	ENSG00000283761	ENST00000638792.1	TSL:5	c.850-686G>A		intron	N/A	ENSP00000491854.1

Frequencies

GnomAD3 genomes AF: 0.220 AC: 33377 AN: 151956 Hom.: 5071 Cov.: 32

Gnomad AFR AF: 0.434

Gnomad AMI AF: 0.196

Gnomad AMR AF: 0.144

Gnomad ASJ AF: 0.124

Gnomad EAS AF: 0.0555

Gnomad SAS AF: 0.0995

Gnomad FIN AF: 0.114

Gnomad MID AF: 0.193

Gnomad NFE AF: 0.150

Gnomad OTH AF: 0.200

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.220 AC: 33437 AN: 152074 Hom.: 5087 Cov.: 32 AF XY: 0.214 AC XY: 15923 AN XY: 74358

African (AFR) AF: 0.434 AC: 17997 AN: 41440

American (AMR) AF: 0.143 AC: 2193 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.124 AC: 429 AN: 3470

East Asian (EAS) AF: 0.0559 AC: 289 AN: 5174

South Asian (SAS) AF: 0.0992 AC: 478 AN: 4820

European-Finnish (FIN) AF: 0.114 AC: 1206 AN: 10578

Middle Eastern (MID) AF: 0.184 AC: 54 AN: 294

European-Non Finnish (NFE) AF: 0.150 AC: 10196 AN: 67992

Other (OTH) AF: 0.197 AC: 416 AN: 2108

Alfa AF: 0.193 Hom.: 793

Bravo AF: 0.231

Asia WGS AF: 0.123 AC: 428 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	8.6
DANN	Benign	0.26
PhyloP100		1.3
Mutation Taster		=100/0	polymorphism (auto)

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: rs560659; hg19: chr1-100523536;