rs7596684

Variant names:

• chr2-112820626-T-C
• rs7596684
• ENST00000670671.2:n.223-1186A>G

Variant summary

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

The ENST00000670671.2(ENSG00000287937):​n.223-1186A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.218 in 152,150 control chromosomes in the GnomAD database, including 3,697 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 0.22 (3697 hom., cov: 32)
• Consequence: ENSG00000287937 ENST00000670671.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.246
• Publications: 12 publications found

Genes affected

ENSG00000287937 (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 (AFR) allele frequency at 95% confidence interval = 0.227 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000670671.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000287937	ENST00000670671.2		n.223-1186A>G		intron	N/A
	ENSG00000299339	ENST00000762706.1		n.404+49730T>C		intron	N/A
	ENSG00000299339	ENST00000762707.1		n.499+49730T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.217 AC: 33059 AN: 152032 Hom.: 3675 Cov.: 32

Gnomad AFR AF: 0.230

Gnomad AMI AF: 0.325

Gnomad AMR AF: 0.171

Gnomad ASJ AF: 0.269

Gnomad EAS AF: 0.0674

Gnomad SAS AF: 0.173

Gnomad FIN AF: 0.246

Gnomad MID AF: 0.339

Gnomad NFE AF: 0.225

Gnomad OTH AF: 0.229

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

GnomAD4 genome AF: 0.218 AC: 33111 AN: 152150 Hom.: 3697 Cov.: 32 AF XY: 0.216 AC XY: 16041 AN XY: 74374

African (AFR) AF: 0.231 AC: 9588 AN: 41478

American (AMR) AF: 0.171 AC: 2609 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.269 AC: 935 AN: 3470

East Asian (EAS) AF: 0.0674 AC: 349 AN: 5178

South Asian (SAS) AF: 0.174 AC: 837 AN: 4822

European-Finnish (FIN) AF: 0.246 AC: 2612 AN: 10602

Middle Eastern (MID) AF: 0.337 AC: 99 AN: 294

European-Non Finnish (NFE) AF: 0.225 AC: 15302 AN: 68000

Other (OTH) AF: 0.229 AC: 484 AN: 2112

Alfa AF: 0.220 Hom.: 5101

Bravo AF: 0.210

Asia WGS AF: 0.131 AC: 456 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.3
DANN	Benign	0.72
PhyloP100		-0.25

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs7596684;

hg19: chr2-113578203;