rs10255878

Variant names:

• chr7-97388483-G-A
• rs10255878
• ENST00000813676.1:n.220-59836C>T

Your query was ambiguous. Multiple possible variants found:

• chr7-97388483-G-A
• chr7-97388483-G-T

Variant summary

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

The ENST00000813676.1(ENSG00000305877):​n.220-59836C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.204 in 152,156 control chromosomes in the GnomAD database, including 3,531 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 0.20 (3531 hom., cov: 32)
• Consequence: ENSG00000305877 ENST00000813676.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.539
• Publications: 4 publications found

Genes affected

ENSG00000305877 (HGNC:58698):

LOC105375416 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.292 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105375416	XR_001745293.1	n.127-59836C>T		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000305877	ENST00000813676.1	n.220-59836C>T		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.203 AC: 30917 AN: 152038 Hom.: 3512 Cov.: 32

Gnomad AFR AF: 0.296

Gnomad AMI AF: 0.162

Gnomad AMR AF: 0.129

Gnomad ASJ AF: 0.171

Gnomad EAS AF: 0.278

Gnomad SAS AF: 0.240

Gnomad FIN AF: 0.160

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.165

Gnomad OTH AF: 0.184

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

GnomAD4 genome AF: 0.204 AC: 30985 AN: 152156 Hom.: 3531 Cov.: 32 AF XY: 0.201 AC XY: 14986 AN XY: 74388

African (AFR) AF: 0.297 AC: 12312 AN: 41482

American (AMR) AF: 0.129 AC: 1978 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.171 AC: 594 AN: 3468

East Asian (EAS) AF: 0.278 AC: 1441 AN: 5176

South Asian (SAS) AF: 0.238 AC: 1149 AN: 4822

European-Finnish (FIN) AF: 0.160 AC: 1699 AN: 10588

Middle Eastern (MID) AF: 0.136 AC: 40 AN: 294

European-Non Finnish (NFE) AF: 0.165 AC: 11232 AN: 68012

Other (OTH) AF: 0.186 AC: 392 AN: 2112

Alfa AF: 0.175 Hom.: 6823

Bravo AF: 0.202

Asia WGS AF: 0.262 AC: 911 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.58
DANN	Benign	0.45
PhyloP100		-0.54

Splicing

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

Other links and lift over

dbSNP: rs10255878; hg19: chr7-97017795;