chr1-150579916-C-G

Variant names:

• chr1-150579916-C-G
• rs3738485
• ENST00000702780.2:n.88C>G

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000702780.2(ENSG00000290074):​n.88C>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.424 in 151,946 control chromosomes in the GnomAD database, including 15,740 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 0.42 (15740 hom., cov: 31)
• Consequence: ENSG00000290074 ENST00000702780.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.21
• Publications: 14 publications found

Genes affected

ENSG00000290074 (HGNC:):

MCL1 (HGNC:6943): (MCL1 apoptosis regulator, BCL2 family member) This gene encodes an anti-apoptotic protein, which is a member of the Bcl-2 family. Alternative splicing results in multiple transcript variants. The longest gene product (isoform 1) enhances cell survival by inhibiting apoptosis while the alternatively spliced shorter gene products (isoform 2 and isoform 3) promote apoptosis and are death-inducing. [provided by RefSeq, Oct 2010]

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.46).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.542 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107985203	NR_186817.1	n.87C>G		non_coding_transcript_exon_variant	Exon 1 of 2
LOC107985203	NR_186818.1	n.87C>G		non_coding_transcript_exon_variant	Exon 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000290074	ENST00000702780.2	n.88C>G		non_coding_transcript_exon_variant	Exon 1 of 1
ENSG00000290074	ENST00000842744.1	n.155C>G		non_coding_transcript_exon_variant	Exon 1 of 2
ENSG00000290074	ENST00000842745.1	n.155C>G		non_coding_transcript_exon_variant	Exon 1 of 3

Frequencies

GnomAD3 genomes AF: 0.424 AC: 64439 AN: 151828 Hom.: 15746 Cov.: 31

Gnomad AFR AF: 0.192

Gnomad AMI AF: 0.533

Gnomad AMR AF: 0.403

Gnomad ASJ AF: 0.385

Gnomad EAS AF: 0.424

Gnomad SAS AF: 0.323

Gnomad FIN AF: 0.624

Gnomad MID AF: 0.396

Gnomad NFE AF: 0.547

Gnomad OTH AF: 0.451

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

GnomAD4 genome AF: 0.424 AC: 64426 AN: 151946 Hom.: 15740 Cov.: 31 AF XY: 0.426 AC XY: 31592 AN XY: 74216

African (AFR) AF: 0.192 AC: 7951 AN: 41494

American (AMR) AF: 0.403 AC: 6149 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.385 AC: 1335 AN: 3472

East Asian (EAS) AF: 0.424 AC: 2168 AN: 5118

South Asian (SAS) AF: 0.324 AC: 1562 AN: 4822

European-Finnish (FIN) AF: 0.624 AC: 6566 AN: 10526

Middle Eastern (MID) AF: 0.398 AC: 117 AN: 294

European-Non Finnish (NFE) AF: 0.547 AC: 37155 AN: 67930

Other (OTH) AF: 0.446 AC: 939 AN: 2106

Alfa AF: 0.474 Hom.: 2305

Bravo AF: 0.397

Asia WGS AF: 0.397 AC: 1381 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.46
CADD	Benign	3.3
DANN	Benign	0.46
PhyloP100		-1.2
PromoterAI		-0.024	Neutral

Splicing

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

Other links and lift over

dbSNP: rs3738485; hg19: chr1-150552392;