rs16865440

Positions:

• chr2-177608681-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000357045.4(ENSG00000237655):​n.85+5508C>T 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 0.0113 in 152,196 control chromosomes in the GnomAD database, including 26 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 0.011 (26 hom., cov: 32)
• Consequence: ENST00000357045.4 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.239

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BS1: Variant frequency is greater than expected in population eas. gnomad4 allele frequency = 0.0113 (1724/152196) while in subpopulation EAS AF= 0.0289 (150/5182). AF 95% confidence interval is 0.0252. There are 26 homozygotes in gnomad4. There are 870 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 26 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000357045.4	n.85+5508C>T		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.0113 AC: 1719 AN: 152078 Hom.: 25 Cov.: 32

Gnomad AFR AF: 0.0248

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00982

Gnomad ASJ AF: 0.00173

Gnomad EAS AF: 0.0289

Gnomad SAS AF: 0.000829

Gnomad FIN AF: 0.00255

Gnomad MID AF: 0.0159

Gnomad NFE AF: 0.00478

Gnomad OTH AF: 0.0124

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

GnomAD4 genome AF: 0.0113 AC: 1724 AN: 152196 Hom.: 26 Cov.: 32 AF XY: 0.0117 AC XY: 870 AN XY: 74412

Gnomad4 AFR AF: 0.0248

Gnomad4 AMR AF: 0.00981

Gnomad4 ASJ AF: 0.00173

Gnomad4 EAS AF: 0.0289

Gnomad4 SAS AF: 0.000830

Gnomad4 FIN AF: 0.00255

Gnomad4 NFE AF: 0.00478

Gnomad4 OTH AF: 0.0128

Alfa AF: 0.00804 Hom.: 2

Bravo AF: 0.0129

Asia WGS AF: 0.0170 AC: 59 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	5.5
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16865440; hg19: chr2-178473409;