rs6735786

Variant names:

• chr2-103153780-C-T
• rs6735786
• ENST00000422683.1:n.213+21727G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000422683.1(ENSG00000229209):​n.213+21727G>A variant causes a intron 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: ENSG00000229209 ENST00000422683.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.70
• Publications: 10 publications found

Genes affected

ENSG00000229209 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000229209	ENST00000422683.1	n.213+21727G>A		intron_variant	Intron 2 of 3	3
ENSG00000300106	ENST00000768846.1	n.66-13818C>T		intron_variant	Intron 1 of 1
ENSG00000300106	ENST00000768847.1	n.52-11046C>T		intron_variant	Intron 1 of 1

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

African (AFR) AF: 0.153 AC: 6367 AN: 41504

American (AMR) AF: 0.421 AC: 6420 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.359 AC: 1247 AN: 3472

East Asian (EAS) AF: 0.648 AC: 3346 AN: 5166

South Asian (SAS) AF: 0.458 AC: 2206 AN: 4816

European-Finnish (FIN) AF: 0.430 AC: 4529 AN: 10540

Middle Eastern (MID) AF: 0.218 AC: 64 AN: 294

European-Non Finnish (NFE) AF: 0.351 AC: 23829 AN: 67968

Other (OTH) AF: 0.345 AC: 727 AN: 2106

Alfa AF: 0.350 Hom.: 41824

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
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs6735786; hg19: chr2-103770238;