chr17-76754249-C-T

Position:

• chr17-76754249-C-T

Variant summary

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

The NM_001242532.5(MFSD11):​c.682+162C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.962 in 578,832 control chromosomes in the GnomAD database, including 270,200 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 0.90 (63552 hom., cov: 30)
  • Exomes 𝑓: 0.98 (206648 hom.)
• Consequence: MFSD11 NM_001242532.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.20

Genes affected

MFSD11 (HGNC:25458): (major facilitator superfamily domain containing 11) 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=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.99 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MFSD11	NM_001242532.5	c.682+162C>T		intron_variant		ENST00000685175.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MFSD11	ENST00000685175.1	c.682+162C>T		intron_variant			NM_001242532.5	P1

Frequencies

GnomAD3 genomes AF: 0.902 AC: 137204 AN: 152038 Hom.: 63532 Cov.: 30

Gnomad AFR AF: 0.671

Gnomad AMI AF: 0.997

Gnomad AMR AF: 0.955

Gnomad ASJ AF: 0.994

Gnomad EAS AF: 0.996

Gnomad SAS AF: 0.984

Gnomad FIN AF: 1.00

Gnomad MID AF: 0.981

Gnomad NFE AF: 0.996

Gnomad OTH AF: 0.921

GnomAD4 exome AF: 0.983 AC: 419284 AN: 426676 Hom.: 206648 Cov.: 5 AF XY: 0.984 AC XY: 222968 AN XY: 226598

Gnomad4 AFR exome AF: 0.677

Gnomad4 AMR exome AF: 0.971

Gnomad4 ASJ exome AF: 0.992

Gnomad4 EAS exome AF: 0.982

Gnomad4 SAS exome AF: 0.983

Gnomad4 FIN exome AF: 1.00

Gnomad4 NFE exome AF: 0.997

Gnomad4 OTH exome AF: 0.965

GnomAD4 genome AF: 0.902 AC: 137269 AN: 152156 Hom.: 63552 Cov.: 30 AF XY: 0.905 AC XY: 67357 AN XY: 74390

Gnomad4 AFR AF: 0.670

Gnomad4 AMR AF: 0.955

Gnomad4 ASJ AF: 0.994

Gnomad4 EAS AF: 0.996

Gnomad4 SAS AF: 0.985

Gnomad4 FIN AF: 1.00

Gnomad4 NFE AF: 0.996

Gnomad4 OTH AF: 0.922

Alfa AF: 0.979 Hom.: 84810

Bravo AF: 0.888

Asia WGS AF: 0.969 AC: 3372 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.80
DANN	Benign	0.45

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs116719; hg19: chr17-74750331;