ENST00000638964.1:n.484+77418G>A

Variant names:

• chr7-12880150-G-A
• rs7795573
• ENST00000638964.1:n.484+77418G>A

Variant summary

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

The ENST00000638964.1(ENSG00000229618):​n.484+77418G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.26 in 151,826 control chromosomes in the GnomAD database, including 5,236 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 0.26 (5236 hom., cov: 32)
• Consequence: ENSG00000229618 ENST00000638964.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.135
• Publications: 1 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=-0.94).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.319 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

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	ENST00000638964.1	TSL:5	n.484+77418G>A		intron	N/A
	ENSG00000229618	ENST00000639998.1	TSL:5	n.483+121834G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.261 AC: 39523 AN: 151708 Hom.: 5241 Cov.: 32

Gnomad AFR AF: 0.262

Gnomad AMI AF: 0.137

Gnomad AMR AF: 0.211

Gnomad ASJ AF: 0.250

Gnomad EAS AF: 0.143

Gnomad SAS AF: 0.333

Gnomad FIN AF: 0.305

Gnomad MID AF: 0.294

Gnomad NFE AF: 0.269

Gnomad OTH AF: 0.265

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

GnomAD4 genome AF: 0.260 AC: 39540 AN: 151826 Hom.: 5236 Cov.: 32 AF XY: 0.264 AC XY: 19554 AN XY: 74184

African (AFR) AF: 0.262 AC: 10875 AN: 41430

American (AMR) AF: 0.211 AC: 3211 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.250 AC: 868 AN: 3470

East Asian (EAS) AF: 0.143 AC: 733 AN: 5138

South Asian (SAS) AF: 0.333 AC: 1599 AN: 4808

European-Finnish (FIN) AF: 0.305 AC: 3206 AN: 10498

Middle Eastern (MID) AF: 0.289 AC: 85 AN: 294

European-Non Finnish (NFE) AF: 0.269 AC: 18286 AN: 67922

Other (OTH) AF: 0.262 AC: 552 AN: 2104

Alfa AF: 0.206 Hom.: 889

Bravo AF: 0.248

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	3.6
DANN	Benign	0.63
PhyloP100		0.14

Splicing

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

Other links and lift over

dbSNP: rs7795573; hg19: chr7-12919775;