rs7095665

Variant names:

• chr10-85544742-G-A
• rs7095665
• XR_946157.3:n.3338-4515C>T

Your query was ambiguous. Multiple possible variants found:

• chr10-85544742-G-A
• chr10-85544742-G-T

Variant summary

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

The XR_946157.3(LOC105378404):​n.3338-4515C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.52 in 151,930 control chromosomes in the GnomAD database, including 20,843 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 0.52 (20843 hom., cov: 32)
• Consequence: LOC105378404 XR_946157.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0870
• Publications: 1 publications found

Genes affected

LOC105378404 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.607 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105378404	XR_946157.3	n.3338-4515C>T		intron_variant	Intron 4 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.520 AC: 78947 AN: 151812 Hom.: 20832 Cov.: 32

Gnomad AFR AF: 0.483

Gnomad AMI AF: 0.469

Gnomad AMR AF: 0.544

Gnomad ASJ AF: 0.506

Gnomad EAS AF: 0.407

Gnomad SAS AF: 0.627

Gnomad FIN AF: 0.442

Gnomad MID AF: 0.674

Gnomad NFE AF: 0.550

Gnomad OTH AF: 0.550

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

GnomAD4 genome AF: 0.520 AC: 79003 AN: 151930 Hom.: 20843 Cov.: 32 AF XY: 0.518 AC XY: 38462 AN XY: 74228

African (AFR) AF: 0.483 AC: 19982 AN: 41404

American (AMR) AF: 0.544 AC: 8311 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.506 AC: 1753 AN: 3462

East Asian (EAS) AF: 0.408 AC: 2099 AN: 5150

South Asian (SAS) AF: 0.625 AC: 3005 AN: 4806

European-Finnish (FIN) AF: 0.442 AC: 4669 AN: 10564

Middle Eastern (MID) AF: 0.663 AC: 195 AN: 294

European-Non Finnish (NFE) AF: 0.550 AC: 37399 AN: 67962

Other (OTH) AF: 0.552 AC: 1163 AN: 2106

Alfa AF: 0.548 Hom.: 11700

Bravo AF: 0.522

Asia WGS AF: 0.542 AC: 1884 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.67
DANN	Benign	0.41
PhyloP100		-0.087

Splicing

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

Other links and lift over

dbSNP: rs7095665; hg19: chr10-87304499;