rs2597279

Variant names:

• chr7-37626246-G-A
• rs2597279
• ENST00000764643.1:n.49-7223C>T

Variant summary

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

The ENST00000764643.1(ENSG00000299559):​n.49-7223C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.696 in 151,420 control chromosomes in the GnomAD database, including 36,843 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 0.70 (36843 hom., cov: 32)
• Consequence: ENSG00000299559 ENST00000764643.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.108
• Publications: 7 publications found

Genes affected

ENSG00000299559 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.723 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000764643.1. 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
	ENSG00000299559	ENST00000764643.1		n.49-7223C>T		intron	N/A
	ENSG00000299559	ENST00000764644.1		n.43-7223C>T		intron	N/A
	ENSG00000299559	ENST00000764645.1		n.149-3907C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.696 AC: 105365 AN: 151302 Hom.: 36818 Cov.: 32

Gnomad AFR AF: 0.730

Gnomad AMI AF: 0.659

Gnomad AMR AF: 0.709

Gnomad ASJ AF: 0.693

Gnomad EAS AF: 0.717

Gnomad SAS AF: 0.733

Gnomad FIN AF: 0.719

Gnomad MID AF: 0.687

Gnomad NFE AF: 0.665

Gnomad OTH AF: 0.712

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

GnomAD4 genome AF: 0.696 AC: 105436 AN: 151420 Hom.: 36843 Cov.: 32 AF XY: 0.700 AC XY: 51827 AN XY: 74014

African (AFR) AF: 0.730 AC: 30225 AN: 41384

American (AMR) AF: 0.710 AC: 10803 AN: 15216

Ashkenazi Jewish (ASJ) AF: 0.693 AC: 2394 AN: 3456

East Asian (EAS) AF: 0.716 AC: 3706 AN: 5176

South Asian (SAS) AF: 0.733 AC: 3537 AN: 4824

European-Finnish (FIN) AF: 0.719 AC: 7581 AN: 10546

Middle Eastern (MID) AF: 0.677 AC: 199 AN: 294

European-Non Finnish (NFE) AF: 0.665 AC: 44903 AN: 67510

Other (OTH) AF: 0.708 AC: 1490 AN: 2106

Alfa AF: 0.658 Hom.: 8219

Bravo AF: 0.702

Asia WGS AF: 0.707 AC: 2440 AN: 3456

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	3.4
DANN	Benign	0.55
PhyloP100		0.11

Splicing

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

Other links and lift over

dbSNP: rs2597279; hg19: chr7-37665849;