rs2700648

Variant names:

• chr3-99388839-G-A
• rs2700648
• ENST00000715235.1:n.52-35671G>A

Variant summary

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

The ENST00000715235.1(ENSG00000243296):​n.52-35671G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.315 in 151,488 control chromosomes in the GnomAD database, including 8,174 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 (8174 hom., cov: 32)
• Consequence: ENSG00000243296 ENST00000715235.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.01
• Publications: 3 publications found

Genes affected

ENSG00000243296 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.443 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000715235.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000243296	ENST00000715235.1		n.52-35671G>A		intron	N/A
	ENSG00000294866	ENST00000726424.1		n.175-16873C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.315 AC: 47721 AN: 151370 Hom.: 8145 Cov.: 32

Gnomad AFR AF: 0.448

Gnomad AMI AF: 0.344

Gnomad AMR AF: 0.269

Gnomad ASJ AF: 0.0929

Gnomad EAS AF: 0.318

Gnomad SAS AF: 0.351

Gnomad FIN AF: 0.287

Gnomad MID AF: 0.203

Gnomad NFE AF: 0.258

Gnomad OTH AF: 0.295

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

GnomAD4 genome AF: 0.315 AC: 47794 AN: 151488 Hom.: 8174 Cov.: 32 AF XY: 0.316 AC XY: 23425 AN XY: 74018

African (AFR) AF: 0.448 AC: 18541 AN: 41372

American (AMR) AF: 0.270 AC: 4091 AN: 15148

Ashkenazi Jewish (ASJ) AF: 0.0929 AC: 321 AN: 3454

East Asian (EAS) AF: 0.318 AC: 1633 AN: 5128

South Asian (SAS) AF: 0.352 AC: 1699 AN: 4824

European-Finnish (FIN) AF: 0.287 AC: 3030 AN: 10544

Middle Eastern (MID) AF: 0.201 AC: 59 AN: 294

European-Non Finnish (NFE) AF: 0.258 AC: 17494 AN: 67714

Other (OTH) AF: 0.292 AC: 613 AN: 2100

Alfa AF: 0.269 Hom.: 5133

Bravo AF: 0.316

Asia WGS AF: 0.354 AC: 1227 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	8.7
DANN	Benign	0.39
PhyloP100		1.0

Splicing

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

Other links and lift over

dbSNP: rs2700648; hg19: chr3-99107683;