rs10905099

Variant names:

• chr10-7047054-A-G
• rs10905099
• ENST00000664549.1:n.191-34398T>C

Variant summary

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

The ENST00000664549.1(ENSG00000287277):​n.191-34398T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0846 in 152,252 control chromosomes in the GnomAD database, including 643 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 0.085 (643 hom., cov: 32)
• Consequence: ENSG00000287277 ENST00000664549.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.224
• Publications: 7 publications found

Genes affected

ENSG00000287277 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0996 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000664549.1. 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
	LOC105376387	NR_188183.1		n.191-34398T>C		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000287277	ENST00000664549.1		n.191-34398T>C		intron	N/A
	ENSG00000287277	ENST00000666104.1		n.136-34398T>C		intron	N/A
	ENSG00000287277	ENST00000668409.1		n.154-34398T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0846 AC: 12874 AN: 152134 Hom.: 642 Cov.: 32

Gnomad AFR AF: 0.102

Gnomad AMI AF: 0.207

Gnomad AMR AF: 0.0776

Gnomad ASJ AF: 0.105

Gnomad EAS AF: 0.000770

Gnomad SAS AF: 0.0446

Gnomad FIN AF: 0.0497

Gnomad MID AF: 0.0886

Gnomad NFE AF: 0.0872

Gnomad OTH AF: 0.0913

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

GnomAD4 genome AF: 0.0846 AC: 12880 AN: 152252 Hom.: 643 Cov.: 32 AF XY: 0.0817 AC XY: 6079 AN XY: 74438

African (AFR) AF: 0.102 AC: 4244 AN: 41548

American (AMR) AF: 0.0775 AC: 1186 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.105 AC: 365 AN: 3468

East Asian (EAS) AF: 0.000772 AC: 4 AN: 5180

South Asian (SAS) AF: 0.0450 AC: 217 AN: 4822

European-Finnish (FIN) AF: 0.0497 AC: 527 AN: 10600

Middle Eastern (MID) AF: 0.0952 AC: 28 AN: 294

European-Non Finnish (NFE) AF: 0.0872 AC: 5929 AN: 68014

Other (OTH) AF: 0.0903 AC: 191 AN: 2114

Alfa AF: 0.0867 Hom.: 1334

Bravo AF: 0.0889

Asia WGS AF: 0.0260 AC: 93 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.3
DANN	Benign	0.49
PhyloP100		-0.22

Splicing

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

Other links and lift over

dbSNP: rs10905099; hg19: chr10-7089016;