rs560659

chr1-100057980-G-A

Variant summary

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

The NM_033055.3(MFSD14A):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: MFSD14A NM_033055.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.33

Genes affected

MFSD14A (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]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MFSD14A	NM_033055.3	c.181-686G>A		intron_variant		ENST00000370152.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MFSD14A	ENST00000370152.8	c.181-686G>A		intron_variant		1	NM_033055.3	P1
	ENST00000432294.1			downstream_gene_variant		3

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

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

Gnomad4 AFR AF: 0.434

Gnomad4 AMR AF: 0.143

Gnomad4 ASJ AF: 0.124

Gnomad4 EAS AF: 0.0559

Gnomad4 SAS AF: 0.0992

Gnomad4 FIN AF: 0.114

Gnomad4 NFE AF: 0.150

Gnomad4 OTH AF: 0.197

Alfa AF: 0.188 Hom.: 733

Bravo AF: 0.231

Asia WGS AF: 0.123 AC: 428 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	8.6
Dann	Benign	0.26

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: rs560659; hg19: chr1-100523536;