rs11153292

Variant names:

• chr6-111401176-G-A
• rs11153292
• NM_001372078.1:c.565+4294C>T

Your query was ambiguous. Multiple possible variants found:

• chr6-111401176-G-A
• chr6-111401176-G-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001372078.1(REV3L):​c.565+4294C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.399 in 151,930 control chromosomes in the GnomAD database, including 14,630 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 0.40 (14630 hom., cov: 32)
• Consequence: REV3L NM_001372078.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.257
• Publications: 8 publications found

Genes affected

REV3L (HGNC:9968): (REV3 like, DNA directed polymerase zeta catalytic subunit) The protein encoded by this gene represents the catalytic subunit of DNA polymerase zeta, which functions in translesion DNA synthesis. The encoded protein can be found in mitochondria, where it protects DNA from damage. Defects in this gene are a cause of Mobius syndrome. [provided by RefSeq, Jan 2017]

MFSD4B (HGNC:21053): (major facilitator superfamily domain containing 4B) Predicted to enable glucose transmembrane transporter activity. Predicted to be involved in glucose transmembrane transport and sodium ion transport. Predicted to be located in apical plasma membrane. 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=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.536 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
REV3L	NM_001372078.1	c.565+4294C>T		intron_variant	Intron 4 of 31	ENST00000368802.8	NP_001359007.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
REV3L	ENST00000368802.8	c.565+4294C>T		intron_variant	Intron 4 of 31	1	NM_001372078.1	ENSP00000357792.3

Frequencies

GnomAD3 genomes AF: 0.399 AC: 60631 AN: 151812 Hom.: 14629 Cov.: 32

Gnomad AFR AF: 0.111

Gnomad AMI AF: 0.503

Gnomad AMR AF: 0.431

Gnomad ASJ AF: 0.428

Gnomad EAS AF: 0.412

Gnomad SAS AF: 0.508

Gnomad FIN AF: 0.498

Gnomad MID AF: 0.396

Gnomad NFE AF: 0.541

Gnomad OTH AF: 0.411

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

GnomAD4 genome AF: 0.399 AC: 60649 AN: 151930 Hom.: 14630 Cov.: 32 AF XY: 0.398 AC XY: 29537 AN XY: 74220

African (AFR) AF: 0.111 AC: 4588 AN: 41452

American (AMR) AF: 0.431 AC: 6578 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.428 AC: 1484 AN: 3468

East Asian (EAS) AF: 0.412 AC: 2126 AN: 5158

South Asian (SAS) AF: 0.510 AC: 2456 AN: 4820

European-Finnish (FIN) AF: 0.498 AC: 5240 AN: 10520

Middle Eastern (MID) AF: 0.418 AC: 123 AN: 294

European-Non Finnish (NFE) AF: 0.541 AC: 36735 AN: 67950

Other (OTH) AF: 0.409 AC: 861 AN: 2106

Alfa AF: 0.437 Hom.: 2125

Bravo AF: 0.380

Asia WGS AF: 0.447 AC: 1552 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.3
DANN	Benign	0.47
PhyloP100		0.26
Mutation Taster		=100/0	polymorphism (auto)

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: rs11153292; hg19: chr6-111722379; COSMIC: COSV62622803; COSMIC: COSV62622803;