rs7606245

Variant names:

• chr2-41790978-C-G
• rs7606245

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 0.31 in 152,038 control chromosomes in the GnomAD database, including 7,548 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 0.31 (7548 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0720
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.372 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.310 AC: 47099 AN: 151920 Hom.: 7524 Cov.: 32

Gnomad AFR AF: 0.377

Gnomad AMI AF: 0.241

Gnomad AMR AF: 0.273

Gnomad ASJ AF: 0.276

Gnomad EAS AF: 0.180

Gnomad SAS AF: 0.249

Gnomad FIN AF: 0.255

Gnomad MID AF: 0.269

Gnomad NFE AF: 0.304

Gnomad OTH AF: 0.281

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

GnomAD4 genome AF: 0.310 AC: 47147 AN: 152038 Hom.: 7548 Cov.: 32 AF XY: 0.308 AC XY: 22867 AN XY: 74330

African (AFR) AF: 0.377 AC: 15640 AN: 41462

American (AMR) AF: 0.273 AC: 4172 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.276 AC: 957 AN: 3464

East Asian (EAS) AF: 0.180 AC: 931 AN: 5176

South Asian (SAS) AF: 0.251 AC: 1210 AN: 4816

European-Finnish (FIN) AF: 0.255 AC: 2700 AN: 10568

Middle Eastern (MID) AF: 0.282 AC: 83 AN: 294

European-Non Finnish (NFE) AF: 0.304 AC: 20647 AN: 67964

Other (OTH) AF: 0.278 AC: 587 AN: 2108

Alfa AF: 0.303 Hom.: 876

Bravo AF: 0.317

Asia WGS AF: 0.241 AC: 843 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.0
DANN	Benign	0.59
PhyloP100		-0.072

Splicing

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

Other links and lift over

dbSNP: rs7606245; hg19: chr2-42018118;