rs2457335

Variant names:

• chr6-20109361-G-A
• rs2457335
• NM_001080480.3:c.1361+237C>T

Your query was ambiguous. Multiple possible variants found:

• chr6-20109361-G-A
• chr6-20109361-G-C
• chr6-20109361-G-T

Variant summary

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

The NM_001080480.3(MBOAT1):​c.1361+237C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.734 in 152,058 control chromosomes in the GnomAD database, including 41,183 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 0.73 (41183 hom., cov: 31)
• Consequence: MBOAT1 NM_001080480.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.971

Genes affected

MBOAT1 (HGNC:21579): (membrane bound O-acyltransferase domain containing 1) This gene belongs to the membrane-bound O-acetyltransferase superfamily. The encoded transmembrane protein is an enzyme that transfers organic compounds, preferably from oleoyl-CoA, to hydroxyl groups of protein targets in membranes. A translocation disrupting this gene may be associated with brachydactyly syndactyly syndrome. Alternately spliced transcript variants have been described for this gene. [provided by RefSeq, Nov 2012]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.928 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MBOAT1	NM_001080480.3	c.1361+237C>T		intron_variant	Intron 12 of 12	ENST00000324607.8	NP_001073949.1
MBOAT1	XM_006714999.3	c.1265+237C>T		intron_variant	Intron 12 of 12		XP_006715062.1
MBOAT1	NR_073465.2	n.1316+237C>T		intron_variant	Intron 9 of 9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MBOAT1	ENST00000324607.8	c.1361+237C>T		intron_variant	Intron 12 of 12	1	NM_001080480.3	ENSP00000324944.7

Frequencies

GnomAD3 genomes AF: 0.734 AC: 111566 AN: 151940 Hom.: 41135 Cov.: 31

Gnomad AFR AF: 0.754

Gnomad AMI AF: 0.499

Gnomad AMR AF: 0.773

Gnomad ASJ AF: 0.634

Gnomad EAS AF: 0.950

Gnomad SAS AF: 0.787

Gnomad FIN AF: 0.783

Gnomad MID AF: 0.693

Gnomad NFE AF: 0.694

Gnomad OTH AF: 0.738

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

GnomAD4 genome AF: 0.734 AC: 111672 AN: 152058 Hom.: 41183 Cov.: 31 AF XY: 0.743 AC XY: 55261 AN XY: 74342

Gnomad4 AFR AF: 0.754

Gnomad4 AMR AF: 0.773

Gnomad4 ASJ AF: 0.634

Gnomad4 EAS AF: 0.950

Gnomad4 SAS AF: 0.787

Gnomad4 FIN AF: 0.783

Gnomad4 NFE AF: 0.694

Gnomad4 OTH AF: 0.741

Alfa AF: 0.711 Hom.: 14887

Bravo AF: 0.734

Asia WGS AF: 0.883 AC: 3066 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.15
DANN	Benign	0.16

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: rs2457335; hg19: chr6-20109592;