rs7005110

Variant names:

• chr8-88748391-A-G
• rs7005110
• ENST00000649573.1:n.141+48042A>G

Variant summary

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

The ENST00000649573.1(ENSG00000253553):​n.141+48042A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.241 in 152,022 control chromosomes in the GnomAD database, including 4,829 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 0.24 (4829 hom., cov: 32)
• Consequence: ENSG00000253553 ENST00000649573.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.308
• Publications: 6 publications found

Genes affected

ENSG00000253553 (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 (AFR) allele frequency at 95% confidence interval = 0.317 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000649573.1. 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
	ENSG00000253553	ENST00000649573.1		n.141+48042A>G		intron	N/A
	ENSG00000253553	ENST00000653184.1		n.144+48042A>G		intron	N/A
	ENSG00000253553	ENST00000659668.1		n.176+48042A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.241 AC: 36649 AN: 151902 Hom.: 4813 Cov.: 32

Gnomad AFR AF: 0.321

Gnomad AMI AF: 0.289

Gnomad AMR AF: 0.307

Gnomad ASJ AF: 0.222

Gnomad EAS AF: 0.189

Gnomad SAS AF: 0.315

Gnomad FIN AF: 0.161

Gnomad MID AF: 0.272

Gnomad NFE AF: 0.189

Gnomad OTH AF: 0.259

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

GnomAD4 genome AF: 0.241 AC: 36700 AN: 152022 Hom.: 4829 Cov.: 32 AF XY: 0.244 AC XY: 18144 AN XY: 74318

African (AFR) AF: 0.321 AC: 13322 AN: 41462

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

Ashkenazi Jewish (ASJ) AF: 0.222 AC: 771 AN: 3466

East Asian (EAS) AF: 0.189 AC: 974 AN: 5156

South Asian (SAS) AF: 0.314 AC: 1514 AN: 4820

European-Finnish (FIN) AF: 0.161 AC: 1701 AN: 10570

Middle Eastern (MID) AF: 0.276 AC: 81 AN: 294

European-Non Finnish (NFE) AF: 0.189 AC: 12833 AN: 67952

Other (OTH) AF: 0.263 AC: 555 AN: 2108

Alfa AF: 0.222 Hom.: 1513

Bravo AF: 0.255

Asia WGS AF: 0.329 AC: 1138 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.51
DANN	Benign	0.77
PhyloP100		-0.31

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs7005110;

hg19: chr8-89760620;