rs6720869

Variant names:

• chr2-76479279-C-T
• rs6720869
• ENST00000798785.1:n.283-24898C>T

Variant summary

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

The ENST00000798785.1(ENSG00000287172):​n.283-24898C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.229 in 152,092 control chromosomes in the GnomAD database, including 4,201 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 0.23 (4201 hom., cov: 33)
• Consequence: ENSG00000287172 ENST00000798785.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.171
• Publications: 3 publications found

Genes affected

ENSG00000287172 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.249 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
ENSG00000287172	ENST00000798785.1	n.283-24898C>T		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.229 AC: 34785 AN: 151974 Hom.: 4198 Cov.: 33

Gnomad AFR AF: 0.177

Gnomad AMI AF: 0.297

Gnomad AMR AF: 0.186

Gnomad ASJ AF: 0.332

Gnomad EAS AF: 0.257

Gnomad SAS AF: 0.200

Gnomad FIN AF: 0.307

Gnomad MID AF: 0.196

Gnomad NFE AF: 0.252

Gnomad OTH AF: 0.222

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

GnomAD4 genome AF: 0.229 AC: 34799 AN: 152092 Hom.: 4201 Cov.: 33 AF XY: 0.231 AC XY: 17166 AN XY: 74338

African (AFR) AF: 0.177 AC: 7354 AN: 41508

American (AMR) AF: 0.186 AC: 2842 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.332 AC: 1149 AN: 3464

East Asian (EAS) AF: 0.257 AC: 1323 AN: 5154

South Asian (SAS) AF: 0.198 AC: 954 AN: 4814

European-Finnish (FIN) AF: 0.307 AC: 3239 AN: 10566

Middle Eastern (MID) AF: 0.207 AC: 61 AN: 294

European-Non Finnish (NFE) AF: 0.252 AC: 17130 AN: 67992

Other (OTH) AF: 0.225 AC: 476 AN: 2114

Alfa AF: 0.225 Hom.: 586

Bravo AF: 0.219

Asia WGS AF: 0.255 AC: 892 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.8
DANN	Benign	0.71
PhyloP100		-0.17

Splicing

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

Other links and lift over

dbSNP: rs6720869; hg19: chr2-76706405;