rs2036358

Positions:

• chr4-16416838-T-C

Variant summary

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

The ENST00000512370.5(ENSG00000248138):​n.105-9527T>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 0.424 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: ENST00000512370.5 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0620

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
LOC105374505	XR_007058068.1	n.133-9527T>C		intron_variant, non_coding_transcript_variant
LOC105374505	XR_007058069.1	n.133-9527T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000512370.5	n.105-9527T>C		intron_variant, non_coding_transcript_variant		2
	ENST00000511818.1	n.36-4222T>C		intron_variant, non_coding_transcript_variant		3

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

Gnomad4 AFR AF: 0.608

Gnomad4 AMR AF: 0.302

Gnomad4 ASJ AF: 0.271

Gnomad4 EAS AF: 0.186

Gnomad4 SAS AF: 0.321

Gnomad4 FIN AF: 0.264

Gnomad4 NFE AF: 0.398

Gnomad4 OTH AF: 0.416

Alfa AF: 0.400 Hom.: 1653

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2036358; hg19: chr4-16418461;