rs116719

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr17-76754249-C-A
• chr17-76754249-C-G
• chr17-76754249-C-T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_024311.5(MFSD11):​c.682+162C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 30)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: MFSD11 NM_024311.5 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: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_024311.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MFSD11	NM_001242532.5	MANE Select	c.682+162C>A		intron	N/A	NP_001229461.1
	MFSD11	NM_001242533.3		c.682+162C>A		intron	N/A	NP_001229462.1
	MFSD11	NM_001242534.3		c.682+162C>A		intron	N/A	NP_001229463.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MFSD11	ENST00000685175.1	MANE Select	c.682+162C>A		intron	N/A	ENSP00000508960.1
	MFSD11	ENST00000336509.8	TSL:1	c.682+162C>A		intron	N/A	ENSP00000337240.3
	MFSD11	ENST00000590514.5	TSL:1	c.682+162C>A		intron	N/A	ENSP00000468309.1

Frequencies

GnomAD3 genomes Cov.: 30

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 426788 Hom.: 0 Cov.: 5 AF XY: 0.00 AC XY: 0 AN XY: 226660

African (AFR) AF: 0.00 AC: 0 AN: 11654

American (AMR) AF: 0.00 AC: 0 AN: 17666

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 13230

East Asian (EAS) AF: 0.00 AC: 0 AN: 28342

South Asian (SAS) AF: 0.00 AC: 0 AN: 41580

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 28520

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 3486

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 257866

Other (OTH) AF: 0.00 AC: 0 AN: 24444

GnomAD4 genome Cov.: 30

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.61
DANN	Benign	0.58
PhyloP100		-1.2
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

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: rs116719; hg19: chr17-74750331;