rs10242595

Variant names:

• chr7-22734612-G-A
• rs10242595

Your query was ambiguous. Multiple possible variants found:

• chr7-22734612-G-A
• chr7-22734612-G-C
• chr7-22734612-G-T

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 0.41 in 151,852 control chromosomes in the GnomAD database, including 14,602 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 0.41 (14602 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.365
• Publications: 35 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.69).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.902 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: 0.410 AC: 62212 AN: 151734 Hom.: 14577 Cov.: 31

Gnomad AFR AF: 0.520

Gnomad AMI AF: 0.391

Gnomad AMR AF: 0.463

Gnomad ASJ AF: 0.518

Gnomad EAS AF: 0.924

Gnomad SAS AF: 0.627

Gnomad FIN AF: 0.229

Gnomad MID AF: 0.662

Gnomad NFE AF: 0.297

Gnomad OTH AF: 0.460

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

GnomAD4 genome AF: 0.410 AC: 62295 AN: 151852 Hom.: 14602 Cov.: 31 AF XY: 0.415 AC XY: 30786 AN XY: 74218

African (AFR) AF: 0.520 AC: 21519 AN: 41352

American (AMR) AF: 0.463 AC: 7075 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.518 AC: 1797 AN: 3468

East Asian (EAS) AF: 0.924 AC: 4775 AN: 5170

South Asian (SAS) AF: 0.627 AC: 3013 AN: 4804

European-Finnish (FIN) AF: 0.229 AC: 2419 AN: 10550

Middle Eastern (MID) AF: 0.651 AC: 190 AN: 292

European-Non Finnish (NFE) AF: 0.297 AC: 20170 AN: 67936

Other (OTH) AF: 0.467 AC: 980 AN: 2100

Alfa AF: 0.356 Hom.: 20439

Bravo AF: 0.434

Asia WGS AF: 0.761 AC: 2641 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.69
CADD	Benign	6.3
DANN	Benign	0.86
PhyloP100		0.36

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs10242595;

hg19: chr7-22774231;