rs7606245

Variant names:

• chr2-41790978-C-G
• rs7606245

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

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

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

Gnomad4 AFR AF: 0.377

Gnomad4 AMR AF: 0.273

Gnomad4 ASJ AF: 0.276

Gnomad4 EAS AF: 0.180

Gnomad4 SAS AF: 0.251

Gnomad4 FIN AF: 0.255

Gnomad4 NFE AF: 0.304

Gnomad4 OTH AF: 0.278

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7606245; hg19: chr2-42018118;