rs6720918

Variant names:

• chr2-122399470-T-A
• rs6720918
• ENST00000657880.2:n.756-133381T>A

Variant summary

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

The ENST00000657880.2(ENSG00000286481):​n.756-133381T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.403 in 152,036 control chromosomes in the GnomAD database, including 12,936 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 0.40 (12936 hom., cov: 32)
• Consequence: ENSG00000286481 ENST00000657880.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.161
• Publications: 4 publications found

Genes affected

ENSG00000286481 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.452 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105373592	XR_001739684.2	n.959+2066T>A		intron_variant	Intron 5 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000286481	ENST00000657880.2	n.756-133381T>A		intron_variant	Intron 3 of 8

Frequencies

GnomAD3 genomes AF: 0.403 AC: 61211 AN: 151916 Hom.: 12929 Cov.: 32

Gnomad AFR AF: 0.399

Gnomad AMI AF: 0.507

Gnomad AMR AF: 0.305

Gnomad ASJ AF: 0.414

Gnomad EAS AF: 0.0166

Gnomad SAS AF: 0.291

Gnomad FIN AF: 0.449

Gnomad MID AF: 0.335

Gnomad NFE AF: 0.456

Gnomad OTH AF: 0.400

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

GnomAD4 genome AF: 0.403 AC: 61256 AN: 152036 Hom.: 12936 Cov.: 32 AF XY: 0.398 AC XY: 29544 AN XY: 74304

African (AFR) AF: 0.399 AC: 16550 AN: 41460

American (AMR) AF: 0.305 AC: 4667 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.414 AC: 1437 AN: 3468

East Asian (EAS) AF: 0.0166 AC: 86 AN: 5174

South Asian (SAS) AF: 0.291 AC: 1401 AN: 4812

European-Finnish (FIN) AF: 0.449 AC: 4743 AN: 10570

Middle Eastern (MID) AF: 0.327 AC: 96 AN: 294

European-Non Finnish (NFE) AF: 0.456 AC: 30977 AN: 67950

Other (OTH) AF: 0.396 AC: 837 AN: 2112

Alfa AF: 0.440 Hom.: 1843

Bravo AF: 0.392

Asia WGS AF: 0.164 AC: 575 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	0.20
DANN	Benign	0.83
PhyloP100		-0.16

Splicing

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

Other links and lift over

dbSNP: rs6720918; hg19: chr2-123157046;