chr2-115848999-T-G

Position:

• chr2-115848999-T-G

Variant summary

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

The ENST00000668438.1(ENSG00000287451):​n.467-13569A>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 0.706 in 151,968 control chromosomes in the GnomAD database, including 38,176 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 0.71 (38176 hom., cov: 31)
• Consequence: ENST00000668438.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0680

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.49).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.75 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000668438.1	n.467-13569A>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.706 AC: 107262 AN: 151850 Hom.: 38145 Cov.: 31

Gnomad AFR AF: 0.651

Gnomad AMI AF: 0.607

Gnomad AMR AF: 0.761

Gnomad ASJ AF: 0.702

Gnomad EAS AF: 0.732

Gnomad SAS AF: 0.666

Gnomad FIN AF: 0.774

Gnomad MID AF: 0.574

Gnomad NFE AF: 0.720

Gnomad OTH AF: 0.715

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

GnomAD4 genome AF: 0.706 AC: 107340 AN: 151968 Hom.: 38176 Cov.: 31 AF XY: 0.708 AC XY: 52566 AN XY: 74270

Gnomad4 AFR AF: 0.651

Gnomad4 AMR AF: 0.761

Gnomad4 ASJ AF: 0.702

Gnomad4 EAS AF: 0.732

Gnomad4 SAS AF: 0.664

Gnomad4 FIN AF: 0.774

Gnomad4 NFE AF: 0.720

Gnomad4 OTH AF: 0.717

Alfa AF: 0.715 Hom.: 22760

Bravo AF: 0.703

Asia WGS AF: 0.676 AC: 2353 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.49
CADD	Benign	15
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs272071; hg19: chr2-116606575;