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 ENST00000511818.1(ENSG00000248138):​n.36-4222T>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 ENST00000511818.1 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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105374505	XR_007058068.1	n.133-9527T>C		intron_variant	Intron 1 of 4
LOC105374505	XR_007058069.1	n.133-9527T>C		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000248138	ENST00000511818.1	n.36-4222T>C		intron_variant	Intron 1 of 3	3
ENSG00000248138	ENST00000512370.5	n.105-9527T>C		intron_variant	Intron 1 of 2	2
ENSG00000248138	ENST00000782749.1	n.148-9527T>C		intron_variant	Intron 1 of 4

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 v4.3

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

Other links and lift over

dbSNP: rs2036358; hg19: chr4-16418461;