chr2-195501166-T-C

Position:

• chr2-195501166-T-C

Variant summary

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

The ENST00000606986.1(ENSG00000271893):​n.263+14271A>G 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 0.327 in 152,092 control chromosomes in the GnomAD database, including 8,225 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 0.33 (8225 hom., cov: 32)
• Consequence: ENST00000606986.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0820

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.385 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000606986.1	n.263+14271A>G		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.328 AC: 49783 AN: 151974 Hom.: 8221 Cov.: 32

Gnomad AFR AF: 0.391

Gnomad AMI AF: 0.161

Gnomad AMR AF: 0.348

Gnomad ASJ AF: 0.285

Gnomad EAS AF: 0.264

Gnomad SAS AF: 0.276

Gnomad FIN AF: 0.333

Gnomad MID AF: 0.250

Gnomad NFE AF: 0.297

Gnomad OTH AF: 0.332

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

GnomAD4 genome AF: 0.327 AC: 49805 AN: 152092 Hom.: 8225 Cov.: 32 AF XY: 0.327 AC XY: 24314 AN XY: 74368

Gnomad4 AFR AF: 0.391

Gnomad4 AMR AF: 0.348

Gnomad4 ASJ AF: 0.285

Gnomad4 EAS AF: 0.263

Gnomad4 SAS AF: 0.276

Gnomad4 FIN AF: 0.333

Gnomad4 NFE AF: 0.297

Gnomad4 OTH AF: 0.332

Alfa AF: 0.300 Hom.: 11227

Bravo AF: 0.335

Asia WGS AF: 0.262 AC: 915 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.4
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4591358; hg19: chr2-196365890;