7-13622389-G-A

Variant names:

• chr7-13622389-G-A
• rs10807768
• ENST00000411542.1:n.352-14257G>A

Variant summary

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

The ENST00000411542.1(ENSG00000229618):​n.352-14257G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.502 in 151,972 control chromosomes in the GnomAD database, including 19,634 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 0.50 (19634 hom., cov: 32)
• Consequence: ENSG00000229618 ENST00000411542.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.539
• Publications: 4 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=-1.01).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.539 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

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
	ENSG00000229618	ENST00000411542.1	TSL:4	n.352-14257G>A		intron	N/A
	ENSG00000229618	ENST00000638964.1	TSL:5	n.724-14257G>A		intron	N/A
	ENSG00000229618	ENST00000639998.1	TSL:5	n.723-14257G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.502 AC: 76200 AN: 151852 Hom.: 19623 Cov.: 32

Gnomad AFR AF: 0.492

Gnomad AMI AF: 0.545

Gnomad AMR AF: 0.456

Gnomad ASJ AF: 0.509

Gnomad EAS AF: 0.157

Gnomad SAS AF: 0.523

Gnomad FIN AF: 0.490

Gnomad MID AF: 0.420

Gnomad NFE AF: 0.544

Gnomad OTH AF: 0.512

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

GnomAD4 genome AF: 0.502 AC: 76267 AN: 151972 Hom.: 19634 Cov.: 32 AF XY: 0.496 AC XY: 36868 AN XY: 74280

African (AFR) AF: 0.492 AC: 20358 AN: 41402

American (AMR) AF: 0.456 AC: 6970 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.509 AC: 1766 AN: 3472

East Asian (EAS) AF: 0.157 AC: 813 AN: 5172

South Asian (SAS) AF: 0.523 AC: 2518 AN: 4818

European-Finnish (FIN) AF: 0.490 AC: 5169 AN: 10540

Middle Eastern (MID) AF: 0.422 AC: 124 AN: 294

European-Non Finnish (NFE) AF: 0.544 AC: 36971 AN: 67966

Other (OTH) AF: 0.513 AC: 1082 AN: 2110

Alfa AF: 0.526 Hom.: 67606

Bravo AF: 0.494

Asia WGS AF: 0.361 AC: 1261 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.58
DANN	Benign	0.41
PhyloP100		-0.54

Splicing

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

Other links and lift over

dbSNP: rs10807768; hg19: chr7-13662014;