XR_007060439.1:n.557+4824G>A

Variant names:

• chr7-95401852-G-A
• rs17880030
• ENST00000718462.1:n.589+4824G>A

Variant summary

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

The XR_007060439.1(LOC107986822):​n.557+4824G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.183 in 152,124 control chromosomes in the GnomAD database, including 3,592 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 0.18 (3592 hom., cov: 32)
• Consequence: LOC107986822 XR_007060439.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.17
• Publications: 1 publications found

Genes affected

ENSG00000233942 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.607 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000718462.1. 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
	ENSG00000233942	ENST00000718462.1		n.589+4824G>A		intron	N/A
	ENSG00000233942	ENST00000818771.1		n.521+4824G>A		intron	N/A
	ENSG00000233942	ENST00000818772.1		n.463+4824G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.183 AC: 27832 AN: 152006 Hom.: 3589 Cov.: 32

Gnomad AFR AF: 0.0634

Gnomad AMI AF: 0.140

Gnomad AMR AF: 0.329

Gnomad ASJ AF: 0.172

Gnomad EAS AF: 0.626

Gnomad SAS AF: 0.275

Gnomad FIN AF: 0.154

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.188

Gnomad OTH AF: 0.201

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

GnomAD4 genome AF: 0.183 AC: 27840 AN: 152124 Hom.: 3592 Cov.: 32 AF XY: 0.190 AC XY: 14152 AN XY: 74364

African (AFR) AF: 0.0632 AC: 2625 AN: 41516

American (AMR) AF: 0.329 AC: 5035 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.172 AC: 596 AN: 3470

East Asian (EAS) AF: 0.625 AC: 3228 AN: 5164

South Asian (SAS) AF: 0.275 AC: 1324 AN: 4818

European-Finnish (FIN) AF: 0.154 AC: 1627 AN: 10574

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

European-Non Finnish (NFE) AF: 0.188 AC: 12803 AN: 67988

Other (OTH) AF: 0.202 AC: 426 AN: 2106

Alfa AF: 0.194 Hom.: 3074

Bravo AF: 0.195

Asia WGS AF: 0.405 AC: 1406 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.38
DANN	Benign	0.67
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs17880030; hg19: chr7-95031164;