rs7778887

Positions:

• chr7-13065384-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000639998.1(ENSG00000229618):​n.484-152161A>G variant causes a intron, non coding transcript 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: ENST00000639998.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.81

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000639998.1	n.484-152161A>G		intron_variant, non_coding_transcript_variant		5
	ENST00000638964.1	n.485-152161A>G		intron_variant, non_coding_transcript_variant		5

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

Gnomad4 AFR AF: 0.388

Gnomad4 AMR AF: 0.307

Gnomad4 ASJ AF: 0.185

Gnomad4 EAS AF: 0.405

Gnomad4 SAS AF: 0.234

Gnomad4 FIN AF: 0.199

Gnomad4 NFE AF: 0.157

Gnomad4 OTH AF: 0.228

Alfa AF: 0.176 Hom.: 4642

Bravo AF: 0.268

Asia WGS AF: 0.293 AC: 1021 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7778887; hg19: chr7-13105009;