rs2036358

Variant names:

• chr4-16416838-T-C
• rs2036358
• ENST00000511818.1:n.36-4222T>C

Variant summary

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

The ENST00000512370.5(ENSG00000248138):​n.105-9527T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.424 in 152,060 control chromosomes in the GnomAD database, including 15,150 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 (15150 hom., cov: 32)
• Consequence: ENSG00000248138 ENST00000512370.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0620
• Publications: 1 publications found

Genes affected

ENSG00000248138 (HGNC:58741):

LOC105374505 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.602 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000512370.5. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000248138	ENST00000511818.1	TSL:3	n.36-4222T>C		intron	N/A
	ENSG00000248138	ENST00000512370.5	TSL:2	n.105-9527T>C		intron	N/A
	ENSG00000248138	ENST00000782749.1		n.148-9527T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.425 AC: 64522 AN: 151942 Hom.: 15147 Cov.: 32

Gnomad AFR AF: 0.609

Gnomad AMI AF: 0.438

Gnomad AMR AF: 0.302

Gnomad ASJ AF: 0.271

Gnomad EAS AF: 0.187

Gnomad SAS AF: 0.320

Gnomad FIN AF: 0.264

Gnomad MID AF: 0.396

Gnomad NFE AF: 0.399

Gnomad OTH AF: 0.421

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

GnomAD4 genome AF: 0.424 AC: 64538 AN: 152060 Hom.: 15150 Cov.: 32 AF XY: 0.413 AC XY: 30722 AN XY: 74316

African (AFR) AF: 0.608 AC: 25223 AN: 41496

American (AMR) AF: 0.302 AC: 4613 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.271 AC: 940 AN: 3472

East Asian (EAS) AF: 0.186 AC: 964 AN: 5176

South Asian (SAS) AF: 0.321 AC: 1547 AN: 4816

European-Finnish (FIN) AF: 0.264 AC: 2773 AN: 10512

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

European-Non Finnish (NFE) AF: 0.398 AC: 27084 AN: 67972

Other (OTH) AF: 0.416 AC: 878 AN: 2110

Alfa AF: 0.407 Hom.: 1787

Bravo AF: 0.436

Asia WGS AF: 0.271 AC: 944 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	3.4
DANN	Benign	0.49
PhyloP100		-0.062

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs2036358;

hg19: chr4-16418461;