rs6735786

Positions:

• chr2-103153780-C-T

Variant summary

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

The ENST00000422683.1(ENSG00000229209):​n.213+21727G>A 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 0.322 in 152,036 control chromosomes in the GnomAD database, including 9,027 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 0.32 (9027 hom., cov: 32)
• Consequence: ENST00000422683.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.70

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.629 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
	ENST00000422683.1	n.213+21727G>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.322 AC: 48971 AN: 151918 Hom.: 9011 Cov.: 32

Gnomad AFR AF: 0.153

Gnomad AMI AF: 0.305

Gnomad AMR AF: 0.420

Gnomad ASJ AF: 0.359

Gnomad EAS AF: 0.649

Gnomad SAS AF: 0.456

Gnomad FIN AF: 0.430

Gnomad MID AF: 0.222

Gnomad NFE AF: 0.351

Gnomad OTH AF: 0.338

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

GnomAD4 genome AF: 0.322 AC: 49013 AN: 152036 Hom.: 9027 Cov.: 32 AF XY: 0.329 AC XY: 24474 AN XY: 74282

Gnomad4 AFR AF: 0.153

Gnomad4 AMR AF: 0.421

Gnomad4 ASJ AF: 0.359

Gnomad4 EAS AF: 0.648

Gnomad4 SAS AF: 0.458

Gnomad4 FIN AF: 0.430

Gnomad4 NFE AF: 0.351

Gnomad4 OTH AF: 0.345

Alfa AF: 0.358 Hom.: 19581

Bravo AF: 0.318

Asia WGS AF: 0.569 AC: 1977 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.26
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6735786; hg19: chr2-103770238;