rs7895870

Variant names:

• chr10-121338735-C-T
• rs7895870

Variant summary

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

The variant allele was found at a frequency of 0.449 in 151,968 control chromosomes in the GnomAD database, including 15,643 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 0.45 (15643 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.00
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.562 is higher than 0.05.

Variant Effect in Transcripts

 

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
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.449 AC: 68191 AN: 151850 Hom.: 15618 Cov.: 32

Gnomad AFR AF: 0.469

Gnomad AMI AF: 0.318

Gnomad AMR AF: 0.450

Gnomad ASJ AF: 0.333

Gnomad EAS AF: 0.579

Gnomad SAS AF: 0.392

Gnomad FIN AF: 0.470

Gnomad MID AF: 0.377

Gnomad NFE AF: 0.437

Gnomad OTH AF: 0.419

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

GnomAD4 genome AF: 0.449 AC: 68262 AN: 151968 Hom.: 15643 Cov.: 32 AF XY: 0.451 AC XY: 33521 AN XY: 74292

African (AFR) AF: 0.469 AC: 19423 AN: 41424

American (AMR) AF: 0.450 AC: 6876 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.333 AC: 1155 AN: 3468

East Asian (EAS) AF: 0.579 AC: 2976 AN: 5140

South Asian (SAS) AF: 0.391 AC: 1883 AN: 4820

European-Finnish (FIN) AF: 0.470 AC: 4968 AN: 10568

Middle Eastern (MID) AF: 0.384 AC: 113 AN: 294

European-Non Finnish (NFE) AF: 0.437 AC: 29693 AN: 67960

Other (OTH) AF: 0.419 AC: 887 AN: 2116

Alfa AF: 0.433 Hom.: 28851

Bravo AF: 0.447

Asia WGS AF: 0.465 AC: 1616 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.017
DANN	Benign	0.56
PhyloP100		-4.0

Splicing

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

Other links and lift over

dbSNP: rs7895870; hg19: chr10-123098249;