rs501700

chr1-100054755-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.181-3911G>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 152,088 control chromosomes in the GnomAD database, including 5,102 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 (5102 hom., cov: 32)
• Consequence: MFSD14A NM_033055.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.53

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• 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.181-3911G>A		intron_variant		ENST00000370152.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MFSD14A	ENST00000370152.8	c.181-3911G>A		intron_variant		1	NM_033055.3	P1

Frequencies

GnomAD3 genomes AF: 0.220 AC: 33455 AN: 151970 Hom.: 5085 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: 0.0559

Gnomad SAS AF: 0.105

Gnomad FIN AF: 0.114

Gnomad MID AF: 0.193

Gnomad NFE AF: 0.150

Gnomad OTH AF: 0.201

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.220 AC: 33516 AN: 152088 Hom.: 5102 Cov.: 32 AF XY: 0.215 AC XY: 15969 AN XY: 74354

Gnomad4 AFR AF: 0.434

Gnomad4 AMR AF: 0.144

Gnomad4 ASJ AF: 0.124

Gnomad4 EAS AF: 0.0563

Gnomad4 SAS AF: 0.105

Gnomad4 FIN AF: 0.114

Gnomad4 NFE AF: 0.150

Gnomad4 OTH AF: 0.198

Alfa AF: 0.162 Hom.: 1372

Bravo AF: 0.231

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	1.7
Dann	Benign	0.56

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: rs501700; hg19: chr1-100520311;