17-76754249-C-T

Variant names:

• chr17-76754249-C-T
• rs116719
• NM_001242532.5:c.682+162C>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 6 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
MFSD11	NM_001242532.5	c.682+162C>T		intron_variant	Intron 8 of 12	ENST00000685175.1	NP_001229461.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MFSD11	ENST00000685175.1	c.682+162C>T		intron_variant	Intron 8 of 12		NM_001242532.5	ENSP00000508960.1

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

African (AFR) AF: 0.677 AC: 7857 AN: 11610

American (AMR) AF: 0.971 AC: 17148 AN: 17658

Ashkenazi Jewish (ASJ) AF: 0.992 AC: 13126 AN: 13226

East Asian (EAS) AF: 0.982 AC: 27828 AN: 28330

South Asian (SAS) AF: 0.983 AC: 40835 AN: 41556

European-Finnish (FIN) AF: 1.00 AC: 28519 AN: 28520

Middle Eastern (MID) AF: 0.961 AC: 3349 AN: 3484

European-Non Finnish (NFE) AF: 0.997 AC: 257038 AN: 257862

Other (OTH) AF: 0.965 AC: 23584 AN: 24430

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

African (AFR) AF: 0.670 AC: 27794 AN: 41458

American (AMR) AF: 0.955 AC: 14600 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.994 AC: 3452 AN: 3472

East Asian (EAS) AF: 0.996 AC: 5156 AN: 5178

South Asian (SAS) AF: 0.985 AC: 4751 AN: 4824

European-Finnish (FIN) AF: 1.00 AC: 10602 AN: 10602

Middle Eastern (MID) AF: 0.980 AC: 288 AN: 294

European-Non Finnish (NFE) AF: 0.996 AC: 67773 AN: 68028

Other (OTH) AF: 0.922 AC: 1944 AN: 2108

Alfa AF: 0.967 Hom.: 108239

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
PhyloP100		-1.2
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs116719; hg19: chr17-74750331;