rs71562288

chr6-111256558-A-G

Variant summary

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

The ENST00000425364.1(MFSD4B-DT):n.105+2372T>C variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.126 in 152,214 control chromosomes in the GnomAD database, including 1,383 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 0.13 (1383 hom., cov: 32)
• Consequence: MFSD4B-DT ENST00000425364.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0290

Genes affected

MFSD4B-DT (HGNC:55773): (MFSD4B divergent transcript)

LOC124901378 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.329 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MFSD4B-DT	XR_001743807.2	n.89+2566T>C		intron_variant, non_coding_transcript_variant
LOC124901378	XR_007059708.1	n.40-280A>G		intron_variant, non_coding_transcript_variant
MFSD4B-DT	XR_001743806.2	n.132+2372T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MFSD4B-DT	ENST00000425364.1	n.105+2372T>C		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.126 AC: 19161 AN: 152096 Hom.: 1381 Cov.: 32

Gnomad AFR AF: 0.130

Gnomad AMI AF: 0.216

Gnomad AMR AF: 0.150

Gnomad ASJ AF: 0.186

Gnomad EAS AF: 0.342

Gnomad SAS AF: 0.0776

Gnomad FIN AF: 0.166

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.0942

Gnomad OTH AF: 0.148

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

GnomAD4 genome AF: 0.126 AC: 19171 AN: 152214 Hom.: 1383 Cov.: 32 AF XY: 0.128 AC XY: 9531 AN XY: 74404

Gnomad4 AFR AF: 0.130

Gnomad4 AMR AF: 0.150

Gnomad4 ASJ AF: 0.186

Gnomad4 EAS AF: 0.342

Gnomad4 SAS AF: 0.0774

Gnomad4 FIN AF: 0.166

Gnomad4 NFE AF: 0.0941

Gnomad4 OTH AF: 0.146

Alfa AF: 0.108 Hom.: 122

Bravo AF: 0.129

Asia WGS AF: 0.200 AC: 691 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
Cadd	Benign	2.9
Dann	Benign	0.79

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs71562288; hg19: chr6-111577761;