chr7-95455087-C-T

Variant names:

• chr7-95455087-C-T
• rs10808093
• ENST00000818771.1:n.640-6452C>T

Variant summary

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

The ENST00000818771.1(ENSG00000233942):​n.640-6452C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.636 in 152,112 control chromosomes in the GnomAD database, including 32,225 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 0.64 (32225 hom., cov: 33)
• Consequence: ENSG00000233942 ENST00000818771.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.249
• Publications: 0 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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.914 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000818771.1. 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
	ENSG00000233942	ENST00000818771.1		n.640-6452C>T		intron	N/A
	ENSG00000233942	ENST00000818772.1		n.464-15605C>T		intron	N/A
	ENSG00000233942	ENST00000818773.1		n.554-6452C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.636 AC: 96634 AN: 151994 Hom.: 32171 Cov.: 33

Gnomad AFR AF: 0.802

Gnomad AMI AF: 0.407

Gnomad AMR AF: 0.642

Gnomad ASJ AF: 0.582

Gnomad EAS AF: 0.937

Gnomad SAS AF: 0.636

Gnomad FIN AF: 0.583

Gnomad MID AF: 0.589

Gnomad NFE AF: 0.524

Gnomad OTH AF: 0.629

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

GnomAD4 genome AF: 0.636 AC: 96750 AN: 152112 Hom.: 32225 Cov.: 33 AF XY: 0.640 AC XY: 47560 AN XY: 74324

African (AFR) AF: 0.803 AC: 33329 AN: 41528

American (AMR) AF: 0.643 AC: 9825 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.582 AC: 2021 AN: 3470

East Asian (EAS) AF: 0.936 AC: 4847 AN: 5176

South Asian (SAS) AF: 0.634 AC: 3056 AN: 4820

European-Finnish (FIN) AF: 0.583 AC: 6164 AN: 10570

Middle Eastern (MID) AF: 0.595 AC: 175 AN: 294

European-Non Finnish (NFE) AF: 0.524 AC: 35630 AN: 67944

Other (OTH) AF: 0.631 AC: 1333 AN: 2112

Alfa AF: 0.559 Hom.: 17619

Bravo AF: 0.652

Asia WGS AF: 0.775 AC: 2693 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.7
DANN	Benign	0.53
PhyloP100		-0.25

Splicing

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

Other links and lift over

dbSNP: rs10808093; hg19: chr7-95084399;