rs7778887

Variant names:

• chr7-13065384-A-G
• rs7778887
• ENST00000638964.1:n.485-152161A>G

Variant summary

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

The ENST00000638964.1(ENSG00000229618):​n.485-152161A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.25 in 151,696 control chromosomes in the GnomAD database, including 5,987 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 0.25 (5987 hom., cov: 32)
• Consequence: ENSG00000229618 ENST00000638964.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.81
• Publications: 3 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=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.39 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000638964.1. 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	ENST00000638964.1	TSL:5	n.485-152161A>G		intron	N/A
	ENSG00000229618	ENST00000639998.1	TSL:5	n.484-152161A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.250 AC: 37842 AN: 151578 Hom.: 5970 Cov.: 32

Gnomad AFR AF: 0.388

Gnomad AMI AF: 0.155

Gnomad AMR AF: 0.306

Gnomad ASJ AF: 0.185

Gnomad EAS AF: 0.404

Gnomad SAS AF: 0.236

Gnomad FIN AF: 0.199

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.157

Gnomad OTH AF: 0.230

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

GnomAD4 genome AF: 0.250 AC: 37904 AN: 151696 Hom.: 5987 Cov.: 32 AF XY: 0.252 AC XY: 18662 AN XY: 74154

African (AFR) AF: 0.388 AC: 15929 AN: 41034

American (AMR) AF: 0.307 AC: 4685 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.185 AC: 643 AN: 3470

East Asian (EAS) AF: 0.405 AC: 2089 AN: 5164

South Asian (SAS) AF: 0.234 AC: 1130 AN: 4828

European-Finnish (FIN) AF: 0.199 AC: 2109 AN: 10582

Middle Eastern (MID) AF: 0.167 AC: 49 AN: 294

European-Non Finnish (NFE) AF: 0.157 AC: 10647 AN: 68020

Other (OTH) AF: 0.228 AC: 482 AN: 2110

Alfa AF: 0.193 Hom.: 9764

Bravo AF: 0.268

Asia WGS AF: 0.293 AC: 1021 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.5
DANN	Benign	0.59
PhyloP100		1.8

Splicing

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

Other links and lift over

dbSNP: rs7778887; hg19: chr7-13105009;