rs2568608

Variant names:

• chr7-13398924-A-C
• rs2568608
• ENST00000411542.1:n.351+88601A>C

Your query was ambiguous. Multiple possible variants found:

• chr7-13398924-A-C
• chr7-13398924-A-T

Variant summary

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

The ENST00000411542.1(ENSG00000229618):​n.351+88601A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.324 in 151,922 control chromosomes in the GnomAD database, including 8,746 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 (8746 hom., cov: 32)
• Consequence: ENSG00000229618 ENST00000411542.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.936
• Publications: 0 publications found

Genes affected

ENSG00000229618 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.464 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000411542.1. 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
	ENSG00000229618	ENST00000411542.1	TSL:4	n.351+88601A>C		intron	N/A
	ENSG00000229618	ENST00000638964.1	TSL:5	n.723+88601A>C		intron	N/A
	ENSG00000229618	ENST00000639998.1	TSL:5	n.722+88601A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.324 AC: 49224 AN: 151804 Hom.: 8728 Cov.: 32

Gnomad AFR AF: 0.469

Gnomad AMI AF: 0.335

Gnomad AMR AF: 0.272

Gnomad ASJ AF: 0.267

Gnomad EAS AF: 0.145

Gnomad SAS AF: 0.230

Gnomad FIN AF: 0.202

Gnomad MID AF: 0.196

Gnomad NFE AF: 0.291

Gnomad OTH AF: 0.300

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

GnomAD4 genome AF: 0.324 AC: 49291 AN: 151922 Hom.: 8746 Cov.: 32 AF XY: 0.316 AC XY: 23490 AN XY: 74264

African (AFR) AF: 0.470 AC: 19456 AN: 41436

American (AMR) AF: 0.271 AC: 4139 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.267 AC: 925 AN: 3470

East Asian (EAS) AF: 0.145 AC: 749 AN: 5172

South Asian (SAS) AF: 0.230 AC: 1111 AN: 4820

European-Finnish (FIN) AF: 0.202 AC: 2129 AN: 10544

Middle Eastern (MID) AF: 0.197 AC: 58 AN: 294

European-Non Finnish (NFE) AF: 0.291 AC: 19786 AN: 67926

Other (OTH) AF: 0.301 AC: 635 AN: 2110

Alfa AF: 0.263 Hom.: 2452

Bravo AF: 0.339

Asia WGS AF: 0.208 AC: 724 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.8
DANN	Benign	0.58
PhyloP100		0.94

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: rs2568608;

hg19: chr7-13438549;