rs1607614

Variant names:

• chr2-35892187-T-G
• rs1607614

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 0.134 in 151,644 control chromosomes in the GnomAD database, including 2,307 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 0.13 (2307 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.255

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.306 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: 0.134 AC: 20327 AN: 151526 Hom.: 2305 Cov.: 32

Gnomad AFR AF: 0.311

Gnomad AMI AF: 0.0691

Gnomad AMR AF: 0.110

Gnomad ASJ AF: 0.0312

Gnomad EAS AF: 0.138

Gnomad SAS AF: 0.128

Gnomad FIN AF: 0.0515

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.0526

Gnomad OTH AF: 0.113

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

GnomAD4 genome AF: 0.134 AC: 20348 AN: 151644 Hom.: 2307 Cov.: 32 AF XY: 0.136 AC XY: 10051 AN XY: 74124

Gnomad4 AFR AF: 0.310

Gnomad4 AMR AF: 0.109

Gnomad4 ASJ AF: 0.0312

Gnomad4 EAS AF: 0.137

Gnomad4 SAS AF: 0.128

Gnomad4 FIN AF: 0.0515

Gnomad4 NFE AF: 0.0526

Gnomad4 OTH AF: 0.113

Alfa AF: 0.0785 Hom.: 370

Bravo AF: 0.144

Asia WGS AF: 0.165 AC: 574 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	9.6
DANN	Benign	0.83

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1607614; hg19: chr2-36117253;